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DottaandClaude Fable 5.2	e8e548e856	feat(db): classify migrations for application under the running release (#20913) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - `packages/db` owns the schema and its migrations. There are 467 migrations, and several ship each day > - A zero-downtime deploy starts the new release while the previous release still serves the same database > - Core does not say whether a migration is safe to apply under the previous release. A deployer must treat each pending migration as a reason to pause, or a person must review it > - On stacks that may not pause, releases wait for hours > - Core owns the schema, so Core must own this knowledge and publish it as data > - This pull request adds a conservative classifier, an in-file override, the published result, and a guard for new migrations > - The benefit is that a deployer can apply routine compatible migrations automatically, and incompatible changes become visible at review time ## Linked Issues or Issue Description **Subsystem affected** Database migrations (`packages/db`), the cloud migrator artifact (`scripts/cloud-migrator-artifacts.mjs`), and the pull-request policy job. **Problem or motivation** Core has no machine-readable statement that a migration can be applied while the previous release still reads and writes the database. A deployer cannot tell an added nullable column from a dropped column. It must pause for both, or refuse the release. **Proposed solution** Classify each migration as `online_compatible`, `requires_staging`, or `unknown`. Publish the result in the migrator manifest. Fail a pull request when a migration it adds is `unknown` and has no reviewed override in the file. **Alternatives considered** - A hand-kept list in the deployer. It goes stale and it is not reviewed with the SQL. - A sibling JSON file in the artifact. It needs a workflow change, and the attestation of `manifest.json` would not cover it. **Roadmap alignment** This is release infrastructure. It adds no product feature. ## What Changed - `packages/db/src/migration-compatibility.ts`: `classifyMigrationSql(sql)` returns `{ compatibility, classified, reasons, override, overrideError }`. It parses statement by statement (breakpoints, `;`, comments, string and dollar quoting, guarded `DO` blocks). A statement that it does not recognize is `unknown`. A migration takes the worst class of its statements. - Lock and duration hazards have their own reason codes (`lock_hazard_*`) and classify as `unknown`, not as compatible with a warning. - Override: `-- paperclip:migration-compat online_compatible: <justification>` (or `requires_staging`) in the leading comment block of the migration file. The justification is mandatory (10 characters or more). A malformed, repeated, or misplaced directive is an error and never improves the verdict. - A table counts as new after a plain `CREATE TABLE`, or after `CREATE TABLE IF NOT EXISTS` when no earlier migration created that table. `classifyMigrationSequence` classifies migrations in apply order with that knowledge. - `packages/db/scripts/migration-compatibility.ts` (run with `pnpm exec tsx` in `packages/db`): classify files, print the distribution, print JSON, or run the guard (`--check`). No new package script. - Published data: `manifest.json` of the cloud migrator artifact has a new additive field `migrationCompatibility`. `version` stays `1`. No existing field changes. The build reads the SQL from the packed `db.tgz`, so the data describes what the migrator applies. `validate` (publisher) and `verify` reject data that is malformed or does not match the packed migrations. The workflow file does not change. - Guard for new migrations: `.github/scripts/check-pr-migration-order.mjs` (the existing "Validate migration ordering against target branch" policy step) now also classifies the migrations that the pull request adds. `check:migrations` runs the same guard against the merge base with `origin/master`, so the `@paperclipai/db` typecheck and build report it locally. `unknown` without an override fails. `requires_staging` prints a notice and passes. A new migration that uses `CONCURRENTLY` also fails when it is not in `MIGRATIONS_WITH_TOP_LEVEL_STATEMENTS` (`packages/db/src/client.ts`), because the migrator would run it inside a transaction. - `doc/DATABASE.md`: new section "Migration compatibility with the running release" under "Schema change workflow". Published shape: ```json "migrationCompatibility": { "version": 1, "migrations": [ { "idx": 468, "tag": "0468_busy_wendell_rand", "sqlSha256": "56a6e272…", "compatibility": "online_compatible", "classified": "online_compatible", "override": false, "reasons": [ { "code": "add_column", "compatibility": "online_compatible", "message": "Adds a column that is nullable or has a constant default.", "statements": [1] } ] } ] } ``` `sqlSha256` is the hash that the migrator records in the migration history. `overrideJustification` is present only when `override` is `true`. Entries are in apply order (journal `idx`, then file name; the shipped journal repeats `idx` 178). ### Distribution over the existing migrations No existing migration is rewritten or annotated. | Class | All 467 | Newest 100 | | --- | --- | --- | | `online_compatible` | 228 (48.8%) | 67 | | `requires_staging` | 114 (24.4%) | 12 | | `unknown` | 125 (26.8%) | 21 | Migrations per blocking reason (one migration can have several): | Migrations | Class | Reason | | --- | --- | --- | | 74 | `requires_staging` | `create_unique_index_existing_table` | | 70 | `unknown` | `lock_hazard_create_index` | | 66 | `unknown` | `lock_hazard_validated_foreign_key` | | 56 | `unknown` | `lock_hazard_data_backfill` | | 54 | `unknown` | `drop_constraint` | | 41 | `requires_staging` | `add_validated_check` | | 33 | `unknown` | `drop_index` | | 16 | `unknown` | `do_block_procedural` | | 15 | `unknown` | `replace_function` | | 13 | `unknown` | `create_trigger_existing_table` | | 12 | `unknown` | `data_change_existing_table` | | 10 | `unknown` | `drop_object`, `lock_hazard_set_not_null`, `set_default` (each) | | 8 | `requires_staging` | `drop_column` | ## Verification - `pnpm --filter @paperclipai/db exec vitest run src/migration-compatibility.test.ts`: 113 tests pass. They cover a positive and a negative case for each rule, each reason code, the override (missing, short, misplaced, and repeated justification are rejected), unknown by default, the guard, the shipped migrations, the `CONCURRENTLY` list, and the command line. - `node --test scripts/cloud-migrator-artifacts.test.mjs .github/scripts/tests/check-pr-migration-order.test.mjs`: 21 tests pass. - Real bundle at the first commit of this branch: `preview-artifacts.mjs pack`, then `cloud-migrator-artifacts.mjs build`, `validate`, and `verify-install` pass. The manifest lists 467 migrations and is 312 KB. This run found the repeated journal `idx`, which the second commit handles. - `pnpm --filter @paperclipai/db run check:migrations` passes. With `--check --base HEAD~150` the guard fails on three `unknown` migrations and prints notices for two `requires_staging` migrations. - `pnpm verify` exits 2 because `.github/scripts/**` is a global CI input. Required CI supplies the broad coverage. - Not run: the publish job (it needs the master-only AWS role), and no deployer reads the new field yet. ## Risks - The manifest grows from about 1 KB to about 312 KB. A consumer that rejects unknown manifest fields would fail. The verifier in this repository ignores unknown fields; consumers outside this repository were not inspected. - From this merge, an open pull request that adds an `unknown` migration fails the policy step and the `@paperclipai/db` typecheck until the author rewrites the migration or adds the override. `drizzle-kit` emits validated foreign keys and plain indexes for existing tables, so this is common. The error text and `doc/DATABASE.md` give the fix. - `ADD CONSTRAINT ... NOT VALID` classifies as `online_compatible`. PostgreSQL still enforces it on new writes, so the author must make sure that the previous release does not write rows that violate it. - The classifier reads SQL only. It cannot see that new code writes values that the previous release cannot read (for example a new enum value). The `requires_staging` override exists for that case. - `master` cannot fail the guard: the guard only judges migrations that are not on the merge base. ## Model Used - Claude (Anthropic), model ID `claude-fable-5-2`, in Claude Code with tool use and code execution. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Fable 5.2 <noreply@anthropic.com>	2026-11-11 14:14:40 -06:00
DottaandPaperclip	cda23f08ac	fix(db): preserve legacy project reads during rolling upgrades (#20860) ... ## Thinking Path > - Paperclip controls agent work while web servers change versions. > - The old and new servers can share a database during that change. > - Older servers still read and write the project environment column. > - Migration 0466 removes that column before those servers stop serving. > - A later repair alone leaves a committed missing-column window and loses values. > - This pull request applies the exact drop and repair in one transaction. > - Old reads and saved values survive while current placement behavior stays unchanged. ## Linked Issues or Issue Description Refs #20835 and #20852. **What happened?** Migration 0466 drops `projects.environment_id`. The previous server still selects that column and reads it during admission. Applying a separate repair afterward leaves a window in which those requests fail. The drop also removes saved values. **Expected behavior** A database that has not yet applied 0466 must keep the column and its values visible to concurrent old servers throughout the upgrade. Both published migration entries must be recorded truthfully. Current project responses must keep the new workspace placement contract. **Steps to reproduce** 1. Use a database before migration 0466 with nonempty project environment values. 2. Keep an old project writer transaction open and start the pending migrator. 3. Start an old project read, then commit the writer. 4. Without this repair, the saved values disappear. With this repair, the reader sees the preserved values and both migrations commit together. ## What Changed - Add migration 0467 to restore the legacy nullable UUID column and its original foreign key. Leave the published 0466 SQL unchanged. - Apply only the exact SHA-bound 0466/0467 pair in one transaction. Lock the project table, retain nonempty values in a temporary table, execute both real SQL files, restore values, and record both real journal entries before commit. - Apply the additive 0467 repair normally when 0466 was already committed. - Keep a deprecated database-only field and omit it from current project API responses. Current placement logic stays unchanged. - Add PostgreSQL regressions for concurrent old reads and writes, idempotence, rollback, and an already-applied drop. Document the overlap contract and retain the five newest generated snapshots. ## Verification - Node 24 cached agent preflight passed. - `pnpm exec vitest run packages/db/src/project-environment-overlap-migration.test.ts server/src/__tests__/project-environments.test.ts -t 'project environment rolling migration|saves storage, not'`: 4 passed in 32.57 seconds against real disposable PostgreSQL. - Before the owner fix, the regression had two failures: saved values disappeared and the restore-failure case committed. The fixed case proves that both DDL and journal entries roll back together. - `pnpm --filter @paperclipai/db typecheck` and `pnpm --filter @paperclipai/db check:migrations`: passed. - `git diff --check`: passed. Migration 0466 bytes are unchanged. The generated snapshot set is 0463 through 0467. - Review found a raw DELETE response that still exposed the database-only field. The delete projection now omits it; a real authorized HTTP DELETE passed with successful cleanup. The concurrency test now observes the old reader waiting inside PostgreSQL before releasing the old writer. All three migration cases passed with that barrier. Earlier HTTP fixture setup/cleanup failures remain recorded as failed attempts; they were not product-regression passes. - Candidate `047178538c0df3a9e382259a51635a6e46da5646` has fresh Greptile 5/5 with no open findings. [Required final-head CI](https://github.com/paperclipai/paperclip/actions/runs/43062354612) passed, including build, typecheck, migration checks, all test shards and the aggregate verification gate. The separate Superagent security scan ended inconclusive/neutral; it did not produce a passed scan. Deployed acceptance remains pending. No hosted database or app deployment was changed by this branch. ## Risks The pair takes a table lock for its transaction. Operators must retain their normal lock and statement timeouts. Both SQL files and their exact hashes must match before the pair runs. A failed restore rolls back the drop and both journal entries. If 0466 was already committed, 0467 restores the column and foreign key. It cannot recover values that were already deleted by the earlier release. This repair does not claim to recover those values. ## Model Used OpenAI Codex (GPT-6), with tool-assisted implementation and real PostgreSQL qualification. The exact serving model ID and context window are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change and contains no internal ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-11 11:08:30 -06:00
DottaandClaude Fable 5.2	464e1de9b1	perf(issues): decide task reads for a list in one batch (#20858) ... The task routes that filter several rows for one actor (summaries, lists, blockers, relation edges and the chat bootstrap) asked for one authorization decision per task, all at the same time. Each decision sent a task-row read and a copy of the task-privacy statement, which is more than 1 KB of SQL, so a request for 50 summaries sent 127 to 279 statements on every pool connection at once. The routes now ask the authorization service for all decisions in one batched read. It reads the task rows and applies the same privacy predicate to all of them in one statement, and reads membership, agent and run policy once. Within a batch, the authorizing user's membership is read once, and the boundary checks of a low-trust agent, which stay per task, run at most eight at a time. A request for 50 summaries now sends 22 to 28 statements (65 for a low-trust agent). Tests compare the batch with one check per task for 24 actors. Co-Authored-By: Claude Fable 5.2 <noreply@anthropic.com>	2026-11-11 10:42:21 -06:00
DottaandClaude Fable 5.2	8ab955776d	perf(github): check the requester provenance of an issue list's review waits in one batch (#20851) ... <!-- Write all pull request text in Simplified Technical English (ASD-STE100): short sentences, one instruction per sentence, simple approved vocabulary, and the active voice. --> ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - An agent can review a GitHub pull request. After the agent publishes the review, the task waits in review for the next GitHub reply. A later run of the same task can inherit this wait. > - Issue lists, issue summaries and inbox attention show these waits. For each waiting task, the server first checks the requester provenance of the waiting run (`chatRunSourceMessageId`). This check is an authorization check: it walks the identity-context lineage of the run and rejects a changed requester, another task, another company or another provider. > - #20673 batched the review reads and the publication reads of one list request. It kept the provenance check as one call for each waiting run, inside `Promise.all`. > - Thus a request with N waits still built and sent at least 2N statements at the same moment. The database is fast for each statement, but the server builds each statement on its main thread. > - On a hosted instance, a CPU profile of the server showed the main thread at 96% of one core. SQL text building, per-statement timers, socket writes and garbage collection had the largest shares. Connection samples showed 235 to 292 pool connections whose last statement was the source-message link read of this check, and 53 to 112 whose last statement was its identity-context read. > - This pull request checks the provenance of all the waiting runs of one request in one batch. The runs that need the same kind of read share one statement. Each run gets the same decision as a separate call, from the same walk and the same reads. > - The benefit is that a list request with 250 waits sends 17 statements, not 658, and uses about one quarter of the CPU time. The statement count no longer follows the number of waits. ## Linked Issues or Issue Description Refs #20673 (batched the review reads and the publication reads of the same request; this change does the same for the provenance reads that #20673 kept for each run). Refs #20551 (authorizes the waits of one issue page with one read). **What happened** `readInheritedGitHubReviewWaits` called `chatRunSourceMessageId` one time for each waiting run, inside `Promise.all`. Each call sent an identity-context read and a source-message link read. A run that continues an earlier run also sent a parent-context read and a source-run read for each continuation in its lineage. `listExternalReviewWaits` calls this function for the issue list, the issue summaries and the inbox attention of a company, so each of those requests repeated the same reads for every waiting task. Evidence from a hosted instance (sanitized): - CPU profile of the server process, 30 s, 5 ms samples: main thread at 96% of one core. Building SQL text for select statements: 17.7% inclusive. The idle-timer restart that the database client does for each statement: 7.6%. Socket writes: 6.2%. Garbage collection: 13%. - Three samples of the pool connections (about 494 connections). 235 to 292 connections had the source-message link read of `chatRunSourceMessageId` as their last statement. 53 to 112 connections had its identity-context read as their last statement. - The `DISTINCT ON` review read that #20673 added ran about 29 times each minute. It runs one time for each list request, so each request started hundreds of provenance reads. **Expected behavior** One list request sends a number of provenance statements that does not follow the number of waiting tasks. The decision for each run does not change. **Steps to reproduce** 1. Put many tasks of one company in review, each with an inherited GitHub review wait. 2. Open the issue list or the inbox. 3. Count the statements that the server sends. The identity-context read and the source-message link read run one time for each waiting task. The benchmark below does these steps on a local PostgreSQL. ## What Changed - `server/src/services/chat-channels/run-origin.ts`: - The provenance decision is now one walk (`sourceMessageWalk`). The walk asks for one read at a time and decides on the returned rows only. Its checks, their order and its error messages are the checks of the previous `chatRunSourceMessageId`. - The five reads of the walk (active identity context, source-message link, board message, parent context, source run) are defined one time in `provenanceReads`. Each definition takes its values either as literals or as SQL columns. - `chatRunSourceMessageId` (single run) drives the walk with one statement for each read, as before. The joins, the company scope and the filters are the same. The identity-context reads now select the seven columns that the walk uses instead of every column. - New `chatRunSourceMessageIds(db, runs, options)` (batch). It drives one walk for each run. In each round, the runs that wait for the same kind of read share one statement: `unnest(...)` of the request values, `CROSS JOIN LATERAL` the same single-row read with the request columns in place of the literals. Thus each run gets the row that its own single read returns, with `LIMIT 1` and the company scope on each join. The result for each run is `{ messageId }` or `{ forbidden }` (the 403 that the single call throws). A database error rejects the whole batch, as `Promise.all` did. - `server/src/services/chat-channels/github/review-wait.ts`: `readInheritedGitHubReviewWaits` checks the provenance of its runs with the batch. A 403 still gives `revoked`. The single-run `readInheritedGitHubReviewWait` does not change. - `server/src/services/chat-channels/run-origin.test.ts`: two new tests (see Verification). - `server/src/__tests__/github-review-wait.test.ts`: one new regression test for the statement count. - `server/scripts/benchmark-review-wait-provenance.ts`: the reproduction and the before/after measurement. It loads the pre-fix modules from `--baseline-ref` and fails unless both versions return the same waits. - `scripts/benchmark-github-review-wait.ts`: removed an assertion that `run-origin.ts` is byte-identical to its baseline. Both sides of that benchmark import the current helper, so the comparison stays fair. Without this change, the documented command of that benchmark fails. - `doc/DATABASE.md`: describes the batch provenance check and the new benchmark command. Statement count of one batch: the walk of one run does at most 3 + 4L reads, where L is the number of continuations in its requester lineage. The batch does the same number of rounds for its longest lineage. Each round sends at most one statement for each kind of read (5 kinds), for any number of runs. A request whose waiting runs accepted their GitHub comment directly sends 2 provenance statements. ## Verification Red/green regression test (`server/src/__tests__/github-review-wait.test.ts`): - `reads the waits of forty runs with the statements of four runs`. Before the fix: `expected { few: 10, many: 82 } to deeply equal { few: 4, many: 4 }`. After the fix: passes. Equivalence tests (`server/src/services/chat-channels/run-origin.test.ts`), on real PostgreSQL: - `gives every run of a batch the decision of its own check, in every provenance state`. 33 runs, each in a different provenance state, are checked with the single function and with the batch for five option sets (no options, legacy wake allowed, GitHub, GitHub with legacy wake, Slack). The test compares the decision of each run (message, `null`, or the 403 and its message) for: the full batch, the reversed batch, and a batch of one run. The states include the negative cases: a run of another company, a message that is linked only in another company, a message that is linked to another task, a conversation that moved to another task, a continuation on another task, a changed requester (run, identity context, continuation, board message), a link of another provider, a missing link, an outbound link only, a deleted message, an agent message, a rejected or pending identity context, a missing parent, another agent and a lineage cycle. The test also states the expected GitHub decision for each state, so the comparison cannot pass on two wrong answers. - `checks the runs of a batch with statements that follow the lineage, not the number of runs`. 4 runs and 40 runs each send 2 statements. 40 separate checks send 80. One continuation in each lineage gives 4 statements for the batch. - A mutation check: when the batch gives a row to the wrong request, both tests fail. Commands: - `pnpm vitest run server/src/services/chat-channels/run-origin.test.ts server/src/__tests__/github-review-wait.test.ts` - Focused run of 15 test files that import the changed modules, their callers or the shared seed helper, including `external-chat-wait.integration.test.ts`, `chat-github-tools.test.ts`, `slack-authority.test.ts` and `issue-list-review-wait-authorization.integration.test.ts`: 482 tests passed. In `idle-completed-history.test.ts`, `afterEach` hooks (a `TRUNCATE` of the test database) timed out at 30 s for 1 test in this run and for 3 tests in a second run of the file, while other agents loaded the machine. No assertion failed. The three tests of that file that reach the changed code pass when they run alone. CI runs the full file. - `server/src/__tests__/chat-channels.integration.test.ts` also uses the single check. It was not run locally (very large file). CI runs it. - Typecheck of the changed files and of the callers of `chatRunSourceMessageId` with a focused `tsc` program: no errors in these files. The full server typecheck was not run locally (shared machine). CI supplies it. - The first CI run of this pull request failed `ci / policy`: the module boundary check rejects an insert into the agents table outside the agent lifecycle module, and the benchmark seeded its fixture agent that way. The second commit seeds that agent with SQL. `pnpm check:module-boundaries` passes locally, and the benchmark gives the same statement counts. - `pnpm verify` returns exit 2 (broader verification required) because the change adds a file under `server/scripts/`. CI supplies the broad coverage. Before/after measurement: ```sh pnpm --filter @paperclipai/server exec tsx scripts/benchmark-review-wait-provenance.ts --baseline-ref=e2cf9a670fc5d5f5058fd0972beb71650f77c554 ``` One call of `listExternalReviewWaits` (the read of one issue list request). Embedded PostgreSQL 18.1, Node v26.4.0, `VACUUM ANALYZE` after seeding. One company, one agent, one GitHub repository. Every wait has a published review. Every tenth waiting run continues three earlier runs. 3 warm-up calls, then 15 pairs in alternating order. Both versions return the same waits and the same inherited wait for each run. | Waits | Version | Statements | SQL text bytes | Wall ms, median (min–max) | CPU ms, median (min–max) | | --- | --- | --- | --- | --- | --- | | 20 | before | 60 | 31,084 | 14.1 (12.8–19.6) | 13.7 (8.7–39.3) | | 20 | after | 17 | 15,847 | 12.5 (9.4–22.7) | 8.8 (4.1–87.1) | | 250 | before | 658 | 300,611 | 63.3 (58.1–89.6) | 78.1 (64.8–103.3) | | 250 | after | 17 | 17,171 | 20.8 (18.9–29.2) | 18.7 (14.1–27.3) | | 1000 | before | 2,608 | 1,179,710 | 256.0 (221.0–363.2) | 303.3 (262.2–507.8) | | 1000 | after | 17 | 21,695 | 54.9 (46.7–81.7) | 51.0 (41.6–72.2) | Of the 658 statements before the fix at 250 waits, 650 are provenance reads: 325 identity-context reads, 250 source-message link reads and 75 source-run reads. After the fix, 9 statements do the same reads. The other 8 statements of the request do not change. Sizes are set with `WAITS=20` and `WAITS=1000`. Other agents used the same machine during the measurement, so the maximum values have noise. - The batch statements use index scans only (`run_identity_contexts_pkey`, `run_identity_contexts_company_run_idx`, `chat_message_links_company_comment_idx`, `chat_conversations_pkey`, `chat_endpoints_company_id_uq`, `heartbeat_runs_pkey`). The 9 batch statements of a request with 250 waits take about 1 ms of server execution in total. - Wall time and CPU time are almost equal before the fix. This shows that the cost is in the server process, not in the database. Not verified: - The effect on the hosted instance. This pull request does not deploy. The share of the main-thread CPU that this path uses there is not known; the profile gives the share of all statement building. ## Risks - The provenance check is an authorization check. The risk is a batch decision that differs from the single decision. Mitigation: both paths run the same walk and build each read from the same definition. The batch read is the single read inside `CROSS JOIN LATERAL`, for each request row. The equivalence test compares both paths in every state. - A database error (for example an invalid UUID in a legacy task binding) rejects the whole batch. The previous `Promise.all` also rejected the whole request. The callers of the batch pass the native task of each run. - The statement count of the batch follows the longest lineage of its runs. A batch with one very long lineage sends as many statements as that run sent before, in sequence. It does not send more. - The batch sends its statements in sequence on one connection. Before, the reads of N runs used up to N pool connections at the same moment. - The single-run callers (GitHub tools, review publication, response comments, Slack authority, the finalizer, the status committer) keep one statement for each read. Their identity-context reads select fewer columns. - No migration. No new index. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - Claude Fable 5.2 (`claude-fable-5-2`), Anthropic, used through Claude Code with tool use (code reading, editing, shell, tests). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Fable 5.2 <noreply@anthropic.com>	2026-11-11 10:19:29 -06:00
DottaandPaperclip	81c9143fe4	fix: upgrade Better Auth to 1.7.16 with account migration (#18906) ... ## Thinking Path > - Paperclip manages AI agents and their work. > - The board uses Better Auth for credential accounts and sessions. > - The server pins Better Auth 1.7.2. > - The November security release fixes 12 issues in Better Auth. > - The new version stops writing the old required account issuer field. > - This change updates the packages and the database contract together. > - New users can sign up, and existing users can still sign in. ## Linked Issues or Issue Description **What happened?** The server uses Better Auth 1.7.2. The [security release](https://better-auth.com/blog/security-release-2026-11-03) fixes 12 issues in 1.7.16. Earlier update PRs #17909 and #17911 target 1.7.7, which is below this security release. **Expected behavior** Use the patched stable release. Keep new and existing credential accounts usable. **Steps to reproduce** Read the server dependency pin. Upgrade it without a schema change. Better Auth then rejects the required account issuer column. See the [upgrade guide](https://better-auth.com/docs/guides/1-7-upgrade-guide). ## What Changed - Pin Better Auth to 1.7.16. The repository refresh bot owns the committed Core lockfile. - Make the old issuer column nullable. Keep existing issuer values. - Replace the issuer index with a unique provider/account index. - Generate the migration and retain the five newest schema snapshots. - Test new signup, new-account sign-in, legacy issuer sign-in, duplicate rejection, and separate provider identities with real PostgreSQL. - Update the database schema test. Test the historical issuer backfill separately. Verify upgrades over existing rows and rollback on duplicate provider/account keys. - Document the duplicate check and migration order. - Add the approved two-line dependency resolution step before the backup job’s frozen install. Leave the frozen check and backup tests intact. ## Verification - Core head: `af70282c7e24335b8688c8f3cc88fdf65045632c`; parent `0f1481e4462100357a7caa496b875cf0bc500d95` includes master `84fc67317`. - Nine changed files. The only workflow edit is the approved two-line backup dependency resolution step; no managed lockfile edits. - Migration `0465_better_auth_account_identity.sql` is three SQL statements; snapshot changes only `public.account`, five newest snapshots retained. - DB typecheck and 23 focused tests passed on the parent. Both real PostgreSQL migration/signup suites were rerun November 11: all 4 tests passed. Application source and tests are unchanged in this workflow-only commit. - The parent’s sandbox-provider lane passed all 205 file-sync tests but reported an unhandled EPIPE during the symlink rejection case; its aggregate verify therefore failed. No unrelated source change was made. The new head reruns the full applicable CI. - Reproduced the old backup install failure locally. Resolving manifests followed by a frozen install passed locally; restored the bot-owned committed lock afterward. Hosted backup qualification remains required. - Current-head CI and review are running; no final-head green claim or merge yet. ## Risks Apply the migration before the new server starts. Check for duplicate provider/account pairs first. Duplicate rows stop index creation. Keep separate users separate when resolving duplicates. The migration keeps issuer data. Do not restore its NOT NULL constraint while new rows contain null. No deployment is included. ## Model Used OpenAI GPT-6 Codex, with reasoning and tool use. The runtime did not expose a more specific model ID or context window. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-11 08:26:58 -06:00
DottaandClaude Opus 5.5	3bf7af6c77	perf(plugins): read the lifecycle inbox from per-resource cursors (#20576) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Plugins get agent, project and agent runtime changes from the `resource_lifecycle_events` journal. Each plugin acknowledges events one resource at a time. > - #20405 made the inbox page read linear in the company journal size. The journal has no retention, so each page still reads every event of the company to find the unacknowledged ones: about 1.7 s per 1M events. > - The delivery worker reads a page again after each acknowledgment. The idle-sleep check also reads the whole journal when all events are acknowledged. `acknowledge` checks every older event of the resource. > - On a hosted instance, the page read ran 181 times in one window at about 1 s each. > - This pull request adds a per-plugin, per-resource cursor. Reads start at the cursor, so they do not read acknowledged history again. > - The benefit is that page, idle-check and acknowledgment cost follow the number of resources and pending events, not the journal size. Delivery order and results stay the same. ## Linked Issues or Issue Description Refs #20405 **What happened?** The plugin lifecycle inbox page query (`select ... from "resource_lifecycle_events" ... DISTINCT ON ...`) ran 181 times at about 1 s each on a hosted database in one window. Each acknowledgment causes another full read of the company journal. The idle-sleep check (`hasPending`) reads the full journal when all events are acknowledged. `acknowledge` reads the full history of the resource. **Expected behavior** A page read, the idle-sleep check and an acknowledgment must not read acknowledged history again. Their cost must not grow with the journal size. **Steps to reproduce** 1. Give a company 400 agents with 2,500 `agent_runtime` events each (1M events). 2. Acknowledge the first 2,000 events of each agent for one plugin. 3. Call `pluginLifecycleInbox(db, pluginId).list(companyId, 100, undefined, ["agent", "project", "agent_runtime"])`. 4. The read takes about 1.7 s. `hasPending` takes about 240 ms. **Paperclip version or commit** `8d2bf78323` (master). **Deployment mode** Hosted (PostgreSQL). Local repro uses embedded PostgreSQL 18. ## What Changed - `packages/db/src/schema/plugin_lifecycle_resource_cursors.ts`: new table `plugin_lifecycle_resource_cursors`. It has one row per plugin, company, resource type and resource id. `acknowledged_through_id` means: every event of that resource at or below this id is acknowledged by the plugin. Plugin and company deletion cascade. - Migration `0462_plugin_lifecycle_resource_cursors`: creates the table and carries existing acknowledgments forward (see Risks for the previous-release story). - `server/src/services/plugin-lifecycle-inbox.ts`: - `list` and `hasPending` use a backward loose index scan on `resource_lifecycle_events_resource_order_idx`. It visits each resource stream once and gets its latest event id. A stream whose latest event is at or below its cursor is settled and is not read again. For other streams, the read gets one head: the unacknowledged creation, else the first unacknowledged transition above the cursor. Then it applies `afterId`, id order and the limit, as before. - `acknowledge` reads only the events between the cursor and the acknowledged event. It still writes the per-event `plugin_lifecycle_acknowledgments` row. It moves the cursor only over a contiguous acknowledged prefix. A creation recorded after a pending transition does not move the cursor. - An event counts as acknowledged when it is at or below the cursor, or when it has an acknowledgment row. Thus rows written by an earlier release, and gaps in old history, keep their current behavior. - `server/src/__tests__/resource-lifecycle-events.test.ts`: new database tests for the migration carry-forward, gaps, late creations, cursor reads, the rollback rows and the plugin-delete cascade. All tests from #20405 still pass without change. - `scripts/benchmark-plugin-lifecycle-inbox.ts`: runs the migration backfill on the fixture and times it. Adds an acknowledgment case. Runs `VACUUM ANALYZE`, because hosted tables are autovacuumed. - `doc/DATABASE.md`: describes the cursor, its read cost and the migration. - The delivery worker (`plugin-lifecycle-delivery.ts`) is not changed. ## Verification Thesis: the cost is a read of the whole company journal (page, idle check) or the whole resource history (acknowledgment). If a per-resource cursor marks the acknowledged prefix, each read can skip that prefix. Then the cost follows the number of resource streams and pending events. The rows must stay equal. Local SQL timings: embedded PostgreSQL 18.1 on Apple Silicon, synthetic data, warm cache, one warmup, 7 samples, baseline and treatment order alternate per sample. The machine was shared with other jobs (load average about 35), so spread is wide. Values are median (min to max) in ms. Rows are equal (`assert.deepEqual`) for every list and probe case. Fixture A: 400 agents x 2,500 runtime events, 2,000 acknowledged per agent. 1,020,440 events, 800,420 acknowledgments. | Case | Before | After | Speedup | | --- | --- | --- | --- | | page of 100, all types | 1,700 (1,633-2,438) | 11.5 (9.5-12.2) | 148x | | page of 100, agent and project | 3.3 (2.5-5.4) | 4.2 (3.6-6.7) | 0.8x (slower) | | idle-sleep check | 238 (174-367) | 2.7 (2.1-3.4) | 88x | | acknowledge one head | 15.3 (9.4-30.1) | 20.3 (12.9-29.9) | neutral (noise) | | migration backfill | - | 9.3 s | - | Fixture B: 40 agents x 25,000 runtime events, 24,000 acknowledged per agent (long history). 1,020,080 events. | Case | Before | After | Speedup | | --- | --- | --- | --- | | page of 100, all types | 1,943 (1,642-4,979) | 4.4 (2.9-5.6) | 444x | | page of 100, agent and project | 3.5 (2.1-5.7) | 4.6 (2.8-12.0) | 0.8x (slower) | | idle-sleep check | 234 (220-243) | 2.8 (1.9-6.5) | 85x | | acknowledge one head | 64.6 (48.5-71.6) | 5.0 (2.6-7.1) | 13x | | migration backfill | - | 4.6 s | - | Fixture C: 5,000 agents x 200 runtime events, 190 acknowledged per agent (many resources). 1,025,040 events. | Case | Before | After | Speedup | | --- | --- | --- | --- | | page of 100, all types | 1,867 (1,649-1,975) | 76.9 (66.2-497) | 24x | | page of 100, agent and project | 10.3 (8.7-12.4) | 21.6 (20.2-23.2) | 0.5x (slower) | | idle-sleep check | 220 (201-298) | 2.8 (2.0-5.3) | 78x | | acknowledge one head | 4.9 (3.4-8.6) | 6.0 (5.2-7.6) | neutral | | migration backfill | - | 15.6 s | - | `EXPLAIN (ANALYZE, BUFFERS)` for the all-types page on fixture A: before 2,488 ms, 13,597 shared hits plus temp files; after 7.0 ms, 7,926 shared hits. Commands: ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-plugin-lifecycle-inbox.ts --baseline-ref=8d2bf78323 --agents=400 --per-agent=2500 --acked=2000 --samples=7 pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-plugin-lifecycle-inbox.ts --baseline-ref=8d2bf78323 --agents=40 --per-agent=25000 --acked=24000 --samples=7 pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-plugin-lifecycle-inbox.ts --baseline-ref=8d2bf78323 --agents=5000 --per-agent=200 --acked=190 --samples=7 cd server && npx vitest run src/__tests__/resource-lifecycle-events.test.ts src/__tests__/plugin-lifecycle-delivery.test.ts src/__tests__/project-instance-secrets.test.ts src/__tests__/agent-runtime-hooks.test.ts pnpm --filter @paperclipai/db check:migrations ``` - `resource-lifecycle-events.test.ts`, `plugin-lifecycle-delivery.test.ts` and `project-instance-secrets.test.ts`: 86 passed. `agent-runtime-hooks.test.ts`: 22 passed. - `tsc --noEmit -p server`: pass. `check:migrations`: pass. ## Risks - **Schema change.** Migration `0462` adds one table and two foreign keys to `plugins` and `companies`. It adds no index on an existing table. The backfill reads the acknowledgment table once. It took 4.6 s to 15.6 s on 1M-event fixtures with 0.8M to 1M acknowledgments. - **Migration order.** The number `0462` is reserved after open PRs that use `0459` to `0461` (#20571, #20568, #20573). Merge this PR after them. Before merge, rebase onto master and chain the snapshot after the latest migration. - **Previous-release story.** - Upgrade: the backfill stores, per plugin and resource, the end of the contiguous acknowledged prefix. A cursor never passes an unacknowledged event, so no event is lost. Acknowledged events above a gap keep their rows, so no event is delivered again. A test runs the migration statement on rows that only an earlier release wrote and checks that `list` returns the same rows before and after. - Rolling deploy: an earlier release that still runs writes only acknowledgment rows. The new reads honor those rows. - Rollback: the new code still writes every acknowledgment row, so an earlier release sees the same progress. - **Ordering assumption.** The cursor is safe because writers record a resource's events while they hold that resource's row lock (`paperclip_record_agent_runtime` locks the agent row; agent status and project writers document the lock). Thus a later commit for the same resource always has a higher id. A writer that breaks this contract could commit an event below the cursor, and that event would not be delivered. A lower id from a different resource is still delivered (existing test). - **Slower path.** A page that asks only for `agent` and `project` streams is 1 to 11 ms slower. These streams are short, so the old full read was cheap, and the new read visits each stream once. The cost is bounded by the number of resources. - **Many resources.** The page cost grows with the number of resource streams of the requested types. At 5,000 agents a page is about 77 ms, compared with about 1.9 s before. - The hosted planner can choose a different plan. The hosted improvement is not yet measured. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude Code with tool use (shell, file edits, local PostgreSQL benchmarks). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 12:58:32 -06:00
DottaandClaude Opus 5.5	8e4c5e81b9	perf(issues): read created-from tasks by index and inbox review waits by page (#20573) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - The task page shows "Created from this task". The inbox shows blocked-inbox attention for a page of tasks. > - On a hosted database, the created-from list ran about 4,000 times in one afternoon at about 499 ms each. The task page sends it each time a task opens. > - Its filter was an `OR` of three provenance paths over the list's own rows. PostgreSQL could not use an index for it. It read every task of the company and tested each one, with the list's other per-row conditions (such as the chat conversation state subquery). > - The blocked-inbox attention map also read external review waits for every in-review task of the company, not only for the tasks of the page. > - This pull request reads created-from tasks from three index probes, and reads review waits only for the in-review tasks that can change a finding of the page. > - The benefit is less database work on each task open and each inbox page. The responses stay the same. ## Linked Issues or Issue Description Refs #20400 (shares review-wait reads between the attention maps of one request). Refs #20551 (authorizes the review waits of a page with one read; this change narrows the waits that the page asks for, and adds a test that pins the batched read). Refs #13241 (adds the created-from list). **What happened** - `GET /api/companies/:id/issues?createdFromIssueId=…` used `createdFromIssueCondition`. Its filter was `origin_issue_id = source OR (origin_issue_id IS NULL AND origin_run_id IN source runs) OR (… AND EXISTS creation activity of a source run)`. The `OR` stops index use, so the statement read every task of the company. The list's other conditions, which include the chat conversation state subquery, ran for each task before the task was excluded. - `listIssueBlockedInboxAttentionMap` read review waits for every in-review task of the company graph. The caller uses the findings of the page rows only. **Expected behavior** The created-from list reads only the created tasks. The blocked-inbox map reads review waits only for in-review tasks that the liveness classifier can read for a page row. The rows, the order, and the attention values do not change. **Steps to reproduce** 1. Use a company with tens of thousands of tasks, runs, and activity rows. 2. Open a task page. Look at the created-from list statement: it reads the full task set of the company. 3. Open an inbox page with blocked-inbox attention. Look at the review-wait read: it gets the ID of every in-review task of the company. ## What Changed - `server/src/services/issue-creation-origin.ts`: `createdFromIssueCondition` is now `issues.id <> source AND issues.id IN (three branches)`. Each branch starts from an index: - recorded origin task: `issues_company_origin_issue_idx`; - legacy origin run: the source task's runs (`heartbeat_runs_company_origin_issue_idx`), then the new partial index on `issues (company_id, origin_run_id)`; - creation activity: `activity_log_run_id_idx` for the source runs, then the task by primary key. The precedence does not change: a recorded origin task wins, the run path applies only without one, and the activity path applies only without both. The activity path matches only an `entity_id` that is the canonical text of the task ID, as before (it also compares `id::text = entity_id`). - `packages/db`: add `issues_company_legacy_origin_run_idx` on `issues (company_id, origin_run_id) WHERE origin_issue_id IS NULL AND origin_run_id IS NOT NULL`. Migration `0461` creates it with `CREATE INDEX CONCURRENTLY IF NOT EXISTS` and is registered with the other concurrent migrations. `doc/DATABASE.md` documents the index and the benchmark command. - `server/src/services/issues.ts`: add `blockedInboxReviewWaitIssueIds`. It returns the in-review tasks in the blocker closure of the page rows. The blocked-inbox map reads review waits only for these tasks. The liveness classifier reads a wait only for a row or for a blocker that it reaches from a row, and the caller reads only the findings of the rows. The classifier does not change. - Tests: - `issue-created-from-routes.test.ts`: new cases for precedence in both directions, a source-run comment, an activity row whose task has another origin run, a non-canonical and a non-UUID activity entity ID, the source's own creation activity, and other-company rows. - `blocked-inbox-review-wait-scope.test.ts`: the narrowed set for chains, cycles, shared blockers and off-page tasks. The rows get the same findings with the narrowed waits as with the waits of every in-review task, and each narrowed wait is needed. - `issue-list-review-wait-authorization.integration.test.ts`: on real PostgreSQL with two authorized waits, `listExternalReviewWaits` and one issue-list request with blocked-inbox attention each send one bound-run message-link statement. With the per-wait authorization from before #20551, both tests fail (2 statements). - `scripts/benchmark-created-from-issues.ts`: local benchmark. It loads the baseline `issues.ts` and `issue-creation-origin.ts` from a pinned commit, asserts identical complete row payloads, and reports alternating timings and `EXPLAIN (ANALYZE, BUFFERS)`. ## Verification - `pnpm --filter @paperclipai/server exec vitest run src/__tests__/issue-created-from-routes.test.ts src/__tests__/blocked-inbox-review-wait-scope.test.ts src/__tests__/issue-list-review-wait-authorization.integration.test.ts src/__tests__/agent-task-hierarchy-depth.test.ts src/__tests__/issue-blocker-attention.test.ts src/__tests__/issue-list-assignee-filter-routes.test.ts src/__tests__/issues-parent-id-alias.test.ts src/__tests__/batched-chat-authorization.integration.test.ts src/__tests__/issue-liveness.test.ts` passes (126 tests). One timing test in `issue-list-assignee-filter-routes` failed one time under machine load and passed on rerun. - `pnpm --filter @paperclipai/server typecheck` and `pnpm --filter @paperclipai/db check:migrations` pass. - `pnpm verify` asks for broader verification because the change adds a file under `scripts/`. Required CI supplies that coverage. - Benchmark: `pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-created-from-issues.ts --baseline-ref=bd30ef8510` Fixture (synthetic, local PostgreSQL 18.1): one company with 30,000 tasks (10,628 with a recorded origin task, 10,445 with only a legacy origin run), 60,030 runs with wide context snapshots (145 MB), and 261,079 activity rows; a second company with 10,000 tasks and 20,000 runs. The busy source task has 63 created tasks through all three paths, plus decoys. The quiet source task has 3. The UI's page: `sortField=id`, `asc`, `limit=500`, routine executions included. Both versions return identical complete payloads. 9 alternating pairs after 2 warm-up pairs: | Case | List statement before | List statement after | List call before, median (min to max) | List call after, median (min to max) | | --- | --- | --- | --- | --- | | Busy source (63 tasks) | 234.9 ms, 47,437 buffers | 0.90 ms, 437 buffers | 156.0 ms (114.5 to 480.7) | 31.6 ms (19.9 to 62.7) | | Quiet source (3 tasks) | 90.7 ms, 47,413 buffers | 0.25 ms, 46 buffers | 126.1 ms (90.6 to 300.4) | 10.5 ms (7.2 to 26.1) | The list call time includes the enrichment reads (labels, runs, attention), which do not change. Inbox page (50 open tasks, blocked-inbox attention): the review-wait read goes from 2 statements with 1,215 parameters (every in-review task of the company) to 1 statement with 31 parameters. The page time does not change in this fixture (median 801 ms before, 873 ms after, both with a wide spread), because the fixture has no review waits and the other graph reads of the map are most of the time. With real waits, the server does an inherited GitHub review read for each wait it finds, so the gain grows with the number of off-page waits. Migration timing (local PostgreSQL 18.1): `0461` (measured as the same statement under its earlier number) on 500,000 tasks (846 MB, 20 companies, one third with a legacy origin run) takes 1.6 s. The index is 12 MB. ## Risks - The new index adds a small write cost to tasks with only an origin run. New tasks with a source task record `origin_issue_id`, so the index holds mostly older tasks. The migration does not lock writes. - The created-from rewrite must keep the same rows. The new tests and the benchmark payload check cover precedence, company scope, and ID text forms. Visibility and read filters are the list's other conditions and do not change. - The review-wait narrowing depends on the liveness classifier reading waits only for rows and their blocker chains. A unit test compares the findings of the rows with full and narrowed waits. A future classifier change that reads waits of other tasks must update `blockedInboxReviewWaitIssueIds`. The function comment says this. - The local timings are synthetic. Hosted acceptance needs a fresh query-statistics window after deployment. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, with tool use (shell, file edits, local PostgreSQL) in Claude Code. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 12:38:51 -06:00
DottaandClaude Opus 5.5	1805a1d247	perf(workspaces): probe workspace run bindings through indexes (#20568) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - The terminal workspace sweep checks each Git workspace for recent activity and for live consumers before it expires or moves the workspace > - These checks find the runs of a workspace with one SQL scope, `expirationScope`. The scope used one `OR` over all run bindings, and one branch decoded the context JSON of each run > - PostgreSQL could not use an index for that `OR`. Each check read every run of the company and its large context from TOAST. On a hosted database, each call took 2 to 5 seconds, about 5,200 s in total in one window > - This pull request splits the scope into one index probe per binding and adds one concurrent expression index for the legacy `executionWorkspaceId` context key > - The benefit is that each check reads a few index entries instead of all company runs. The cleanup decisions do not change ## Linked Issues or Issue Description **What existing behavior does this improve?** The workspace activity and cleanup-safety checks: `gitWorkspaceLastActivityAt`, `isGitWorkspaceExpirationEligible`, `workspaceMoveEligible` and the orphan-folder consumer check. All of them use `expirationScope` in `server/src/services/git-workspace-expiration.ts`. **Subsystem affected** Execution workspace cleanup in the server (`git-workspace-expiration.ts`, `isolated-repository-rehome.ts`, `isolated-task-directory-retention.ts` through the shared scope) and the `heartbeat_runs` schema in `packages/db`. **Current behavior** The `relevant_runs` CTE selects company runs where any of these is true: `issue_id` or `native_issue_id` is in the issue tree or the bound issues, the run is a bound issue's checkout or execution run, or the context JSON has a matching `issueId`, `taskId` or `executionWorkspaceId`. The planner does one sequential scan of the company runs and reads each context from TOAST. The cost grows with the run history of the company, not with the size of the workspace. **Proposed behavior** Each binding is a separate index probe. The `UNION` of run IDs goes to a primary-key probe. The SQL gives the same rows. **Reason and benefit** Local SQL measurements show a 34x to 169x decrease in time. The decrease grows with the run history (see Verification). ## What Changed - `expirationScope` builds `relevant_runs` from a `UNION` of index probes, one for each binding. The key sets go in as arrays (`= ANY(ARRAY(...))`). With `IN (subquery)`, the planner chose a hash join over a full scan, because it does not count the cost of reading TOASTed contexts. - The legacy context keys use `context_snapshot ->> 'key'`. This expression matches the existing indexes `heartbeat_runs_company_ctx_issue_created_idx` and `heartbeat_runs_company_ctx_task_created_idx`. For a non-object context, `->>` gives `NULL`, as the strict JSONPath decode did. Such a run can still match through a native binding. - New partial index `heartbeat_runs_company_ctx_execution_workspace_idx` on `(company_id, context_snapshot ->> 'executionWorkspaceId') WHERE context_snapshot ? 'executionWorkspaceId'`. The query repeats the predicate. For an array context, `?` can be true, but `->>` gives `NULL`, so the result does not change. The index is partial so that it serves only this probe. A full index that starts with `company_id` made the planner choose it for an unrelated company-scoped query. Migration 0460 builds it with `CREATE INDEX CONCURRENTLY IF NOT EXISTS`. The migration is in the list of migrations that run outside a transaction. - New tests: a legacy `issueId` or `executionWorkspaceId` binding on a run that is bound to a different issue still blocks cleanup. A plan test with `enable_seqscan = off` checks that no binding scans `heartbeat_runs` and that the three context indexes are used. - The benchmark script `scripts/benchmark-workspace-activity.ts` gets a `--runs-per-workspace` option. Unrelated fixture runs now have distinct context IDs, as real history does. - `doc/DATABASE.md` describes the probes and the new index. ## Verification - `pnpm --filter @paperclipai/server exec vitest run src/__tests__/git-workspace-activity.test.ts src/__tests__/native-harness-backup-expiration.test.ts`: 132 of 132 tests pass. The second file checks that the native session index stays the planner's choice for its query. These include the existing route matrix (root, child, bound, native, context issue, context task, context workspace, checkout, execution run), exactly-once counts, malformed and uppercase contexts, company isolation, controller leases and lease vetoes. - `pnpm --filter @paperclipai/server typecheck` and `pnpm --filter @paperclipai/db check:migrations` pass. - Benchmark (local SQL measurement, PostgreSQL 18.1, synthetic fixture, 8 workspaces per sample, before and after alternate in each iteration). The script compares the complete ordered caller results and the complete `relevant_runs` multisets of the baseline and treatment. They are equal in every run. `pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-workspace-activity.ts --baseline-ref=origin/master --runs-per-workspace=<N>` | Fixture | Check | Before median (min–max) | After median (min–max) | Speedup | | --- | --- | --- | --- | --- | | 4,800 runs, 330 MB | last activity | 523 ms (460–598) | 12 ms (8–15) | 44x | | 4,800 runs, 330 MB | eligibility | 452 ms (432–473) | 13 ms (11–15) | 34x | | 4,800 runs, 330 MB | idle eligibility | 465 ms (442–573) | 12 ms (10–13) | 40x | | 24,000 runs, 1.7 GB | last activity | 2,240 ms (2,214–2,454) | 13 ms (11–14) | 169x | | 24,000 runs, 1.7 GB | eligibility | 2,245 ms (2,097–2,377) | 17 ms (14–19) | 133x | | 24,000 runs, 1.7 GB | idle eligibility | 2,196 ms (2,179–2,381) | 15 ms (13–18) | 143x | Before: one `Seq Scan` on `heartbeat_runs`. After: `heartbeat_runs_company_issue_created_idx`, `heartbeat_runs_company_native_issue_contract_id_uq`, the three context indexes and `heartbeat_runs_pkey`. - Index build time: on a synthetic table with 200,000 runs and 8 KiB contexts (1.8 GB), the full form of this index took 3.7 s to build concurrently and used 15 MB. The partial index reads the same rows and holds only runs that have the key. ## Risks - Cleanup safety: a wrong "allowed" result could delete an active workspace. The scope keeps every binding of the old query. The benchmark checks exact equality of the run sets, and the existing tests check each binding route and each veto. - Migration: the index build reads every run context once. It runs concurrently and does not block writes. Until migration 0460 builds the index, the new query is still correct but the `executionWorkspaceId` probe scans. - Plan choice: the array form makes index probes the cheapest plan for a small tree. A very large issue tree gives a large array, but each element is still one index probe. - The sweep frequency does not change. This pull request reduces only the cost of each check. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, with tool use and code execution in Claude Code. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 12:17:46 -06:00
DottaandClaude Opus 5.5	d5c1f48180	perf(native): index the backup lease lookup by scope digest (#20571) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Native harness backup expiration removes old session backups. Before it removes a backup, it finds the environment leases that reference the backup root > - This lookup reads leases by run ID, by the `metadata.nativeHarnessBackup.sessionScopeSha256` digest, or by the identity's own lease ID, in one `OR` query > - The metadata arm has no index. So PostgreSQL reads every lease of the company, and the metadata of each lease, for each lookup > - On a hosted test database, this statement ran 21,736 times at a mean of 158 ms in one window. After other fixes, it still ran 2,364 times at a mean of 121 ms > - This pull request adds a small partial expression index on the digest > - The benefit is that each lookup reads a few index entries instead of all company leases. The query text and the result do not change ## Linked Issues or Issue Description **What existing behavior does this improve?** The lease lookup in `backupDependencies` in `server/src/services/native-runtime/native-harness-backup-expiration.ts`. `reconcileBackup` calls it for each backup root when the expiration worker loads or checks a root. **Subsystem affected** Native harness backup expiration and the `environment_leases` table schema. **Current behavior** The query is `company_id = $1 and (heartbeat_run_id in (...) or metadata->'nativeHarnessBackup'->>'sessionScopeSha256' = $n or id = $m)`. The run arm and the ID arm have indexes. The digest arm has no index. A `BitmapOr` plan needs an index for every arm, so the planner reads all company leases and evaluates the JSON expression on each row. Lease metadata holds sandbox details, so these reads are large. **Proposed behavior** The partial index `environment_leases_native_backup_scope_idx` keys leases by the digest. It holds only leases that have a backup stamp. Every arm of the `OR` now has an index, and the planner combines three index probes. The SQL and the returned lease IDs do not change. **Reason and benefit** This statement was in the top ten by total database time on a loaded hosted database. A local reproduction shows a query that is more than 6,000x faster and reads 9 buffers instead of about 436,000. **Breaking changes** None. The API, the lease-matching rules and the results do not change. ## What Changed - Add the partial expression index `environment_leases_native_backup_scope_idx` on `(metadata->'nativeHarnessBackup'->>'sessionScopeSha256')`, where that value is not null. - Add migration `0459`. It uses `CREATE INDEX CONCURRENTLY IF NOT EXISTS`. The migration runner runs it as a top-level statement, the same as migrations 0454–0458. - Add a regression test. It checks the lease-matching rules: run leases, a lease with only the backup stamp, and the identity's own lease match. Another digest, a non-string stamp, a top-level key with the same name, and the same digest in another company do not match. The test also checks that the custom plan and a forced generic plan of the generated SQL use `BitmapOr` with the new index and no sequential scan. - Add `scripts/benchmark-environment-lease-backup-lookup.ts`. It captures the SQL that the real service generates and measures it with and without the index. - Document the index in `doc/DATABASE.md`. ## Verification Cause and thesis. The cost comes from the one `OR` arm without an index, which forces a scan of all company leases and their metadata. Thesis: an index on the digest lets the planner use a `BitmapOr` of three index probes, so the cost no longer depends on the company's lease count. The results stay identical. The benchmark confirms the thesis. I did not change the SQL. With the index, the existing `OR` query already gets the index plan. A `UNION` rewrite would not help without the index, because the digest arm would still scan the company. Local SQL benchmark: ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-environment-lease-backup-lookup.ts ``` Fixture (synthetic): one company with 100,000 leases with 4 KiB of incompressible metadata each. 30% of the leases have a backup stamp for another session. A second company has 20,000 leases. The table is 678 MB. The backup root has 3 run leases, 1 lease with only the stamp, and 1 identity lease. The same digest is also in the other company. Embedded PostgreSQL 18 on an Apple laptop, which other work loaded heavily. The hosted database is Neon with different compute, so absolute times are local SQL measurements only. The script measures in the order: no index, index, no index, index. Each measurement has 2 warmups and 11 samples of `EXPLAIN ANALYZE` execution time and of the full `reconcileBackup` call. | Measurement | Without index | With index | | --- | --- | --- | | Lease query execution, run 1 | median 196 ms (138–562 ms) | median 0.010 ms (0.007–0.017 ms) | | Lease query execution, run 2 | median 185 ms (144–295 ms) | median 0.030 ms (0.020–0.045 ms) | | `reconcileBackup` wall time (includes file reads), runs 1 and 2 | median 188 ms and 216 ms | median 1.4 ms and 4.2 ms | | Plan | `Gather > Seq Scan` | `Bitmap Heap Scan > BitmapOr` of `heartbeat_run_idx`, the new index and `pkey` | | Buffers | 365,880 hit + 70,050 read | 9 hit | These numbers are from head `65bd9d7ac6`. The final head only renumbers the migration to 0459 after rebases; the SQL, the index and the service code are the same. Two earlier runs on the same fixture, SQL and index gave 236–425 ms without the index and 0.023–0.033 ms with the index. The machine had heavy load from other work, so the spread without the index is wide. Output check: in all four measurements, the service returned the same 5 lease IDs, and the complete query rows were equal. Index build (`CREATE INDEX CONCURRENTLY` from the migration file): 0.8–2.4 s for the 678 MB table over all runs. Index size: 3.4 MB with 30% of leases stamped. Tests: - `cd server && npx vitest run src/__tests__/native-harness-backup-expiration.test.ts`: 109 passed. The new test failed when I dropped the index before the plan check (confirmed red), and it passes with the index. - `pnpm --filter @paperclipai/db check:migrations`: passed. - `pnpm --filter @paperclipai/db typecheck` and `pnpm --filter @paperclipai/server typecheck`: passed. - `pnpm verify`: it asks for broader coverage (exit 2) because of the new script. See the CI results for this head. ## Risks - Migration time. A concurrent index build reads the full `environment_leases` table and does not block writes. Locally, the build took 0.8–2.4 s for 678 MB. The time grows linearly with the table size. I did not time it on a production-size clone. I expect a few seconds to tens of seconds on a large instance, which is in the 1–2 minute budget. This estimate is not proven. - If the build stops, PostgreSQL can leave an invalid index. The migration runner repairs invalid concurrent indexes when it runs again, and `IF NOT EXISTS` makes a rerun safe. - The index expression must stay textually equal to the query expression. If someone changes the JSON path, the planner cannot use the index. The new test catches this for custom and generic plans. - The index is partial, so ANALYZE does not collect statistics for the expression. The planner uses the default equality estimate. On the large fixture and in the small test, the planner still selects the index plan. A company with very few leases can still get a sequential scan, which is cheap. - Each lease write with a backup stamp writes one more small index entry. The write cost is small. - This change does not reduce how often the worker calls the lookup. It makes each call cheap. The other digest lookups in backup retention (`native-harness-backup-retention.ts`) and session retention checks can also use the index. - Previous-release story: no persisted state changes. The index is derived from existing lease metadata. - The hosted improvement is not verified until deployment. After deployment, compare a new query-statistics window for this statement. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude Code with tool use (shell, file edits, local PostgreSQL benchmarks). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 11:30:05 -06:00
DottaandClaude Opus 5.5	6ed6b0754b	perf(recovery): probe recovery source runs and stale-continuation runs by key (#20584) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - The workspace recovery worker saves the files of failed runs. After each pass, it reads the time of its next deadline (`nextWorkspaceRecoveryAt`) > - That read finds the source run, its finalizer and its leases with `id::text = evidence->>'runId'`. A text comparison cannot use a key. Each exhausted hold read every run, finalizer and lease of its company > - On a hosted staging database this statement used about 4 s per call (21 calls in the sample window). The cost grows with exhausted holds multiplied by the company's run count > - The ownership reconciler's stale-continuation check (`checkStaleDroppedComments`) has the run lookup shape that #20412 fixed in the lost-wake check: one OR across the legacy context and the native column > - This pull request compares the run id as a canonical uuid, and it gives the stale-continuation check the per-binding run probes from #20412 > - The benefit is the same recovery decisions with index-driven work: 11 s to 93 ms for the deadline read on a representative local fixture ## Linked Issues or Issue Description Refs #20412 **What happened?** The workspace recovery deadline read was one of the most expensive statements that remained on a hosted staging database after the fixes in #20393, #20405, #20386, #20412, #20391 and #20400. Query statistics showed about 4 s per call. The statement text starts with `select case when (issue_recovery_actions.…`. The statement evaluates the retained-source fallback and stop-proof conditions for each recovery action. These conditions read the source run (`heartbeat_runs`), its finalizer (`native_run_finalizations`) and its leases (`environment_leases`) with `x.id::text = evidence->>'runId'`. The cast prevents the use of the primary key. PostgreSQL reads all rows of the company for each exhausted hold. The worker's discovery (`retainedWorkspaceCandidates`) uses the same conditions. The stale-continuation check matched a task's runs with `(context_snapshot->>'issueId' = issue OR native_issue_id = issue)`. With the OR, PostgreSQL can join runs only by company. It also hashed every wake request of the company for the stale-wake test. **Expected behavior** Each condition uses a key lookup. The worker and the reconciler make the same decisions for the same saved state. **Steps to reproduce** 1. Seed a company with a deep run history and a few thousand workspace recovery actions. Let a few hundred be exhausted holds that stay active. 2. Call `nextWorkspaceRecoveryAt`. 3. The call takes seconds, and its time grows with holds multiplied by runs. The benchmark below shows this. **Paperclip version or commit** Baseline: `8d2bf78323`. **Deployment mode** Server with PostgreSQL. The local proof uses disposable PostgreSQL 18.1. Staging uses hosted PostgreSQL. ## What Changed - `workspace-recovery-fallback-discovery.ts`: the source run, finalizer and lease probes compare `id = canonicalExecutionUuid(evidence->>'runId')`. The helper returns null unless the text is the canonical lowercase uuid form. Thus the probe matches exactly the rows that `id::text = evidence->>'runId'` matched. The helper already exists in `execution-identity.ts`. - `nextWorkspaceRecoveryAt` and worker discovery use these conditions. Their SQL changes only in these probes. - `checkStaleDroppedComments` reads in two stages. The first stage keeps comments that a stale-continuation cancellation dropped and that no open wake carries. The second stage applies the run probes. The run probes use the `taskRuns` helper from #20412, which is now shared by both checks. The stale-wake lookup ends with `offset 0`, so it stays a per-comment index probe. - The final `order by c.created_at limit N`, the projection and the delivery check after the query do not change. - Add `scripts/benchmark-recovery-status-checks.ts`. It loads the changed files from an explicit baseline commit and from the working tree. Before it records time, it compares every changed condition for every recovery action, the complete service results and the positional SQL rows. - Add tests: each run binding in the stale-continuation check (native, legacy, live run on either binding, wrong agent, wrong company, failed run, run outside the comment time, closed by a person, open wake). Also a test that a hold with a non-canonical saved run id is not discovered, as before. - Document both checks and the benchmark in `doc/DATABASE.md`. - No schema change, index, migration, or new startup work. ## Verification - `pnpm exec vitest run src/__tests__/ownership-reconciliation-report.test.ts src/services/workspace-recovery-fallback.test.ts src/services/workspace-recovery-stop-proof.test.ts src/__tests__/heartbeat-held-comment-wake.test.ts --maxWorkers=1` (from `server/`). - `pnpm --filter @paperclipai/server typecheck`. - `pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-recovery-status-checks.ts --baseline-ref=8d2bf78323 --samples=7` Benchmark setup: PostgreSQL 18.1 (embedded, local), `shared_buffers` 128 MB, `work_mem` 4 MB. All data is synthetic, with md5-hex filler. Each fixture has two companies (full size and a quarter). Two warmup rounds, then 7 timed samples for each arm, in alternating order. Each sample runs the real service function and asserts the same result. These are local SQL measurements on a shared machine, so the spread is wide. Workspace recovery deadline (`nextWorkspaceRecoveryAt`). About 8% of actions are exhausted holds that stay active. Some actions save a non-canonical (uppercase) run id. Before timing, the benchmark compares six conditions (fallback pending, due time, due; re-arm pending, due time, due) for every action of the fixture. | Fixture | Runs / actions / pending holds | Baseline median (min–max) | Treatment median (min–max) | Shared buffers | | --- | --- | --- | --- | --- | | small | 6,500 / 255 / 36 | 50.9 ms (47–76) | 6.8 ms (6–8) | 19,133 → 1,075 | | representative | 78,750 / 3,813 / 588 | 11,098 ms (8,277–12,790) | 93 ms (35–145) | 3,493,417 → 24,902 | | deep history | 191,250 / 3,813 / 588 | 40,146 ms (31,190–52,521) | 40 ms (36–230) | 13,491,792 → 26,911 | Stale-continuation check (`checkStaleDroppedComments`). The fixture is pessimistic: more than half of recent comments on done tasks have a stale cancelled wake. The table shows statement time from `EXPLAIN ANALYZE` with default settings, and one statement run with `enable_nestloop = off` (the company-only hash plan). The result is checked as equal in both modes. | Fixture | Runs / recent comments / reported | Statement, baseline → treatment | Hash plan, baseline → treatment | | --- | --- | --- | --- | | small | 3,792 / 76 / 24 | 3.2 → 1.5 ms | 5.5 → 3.8 ms | | representative | 75,406 / 1,125 / 200 (limit) | 34 → 26 ms | 66 → 25 ms | | busy hour | 152,031 / 5,625 / 200 (limit) | 328 → 153 ms | 2,302 → 165 ms | - Neutral path: the complete stale-continuation service call stays about the same (busy hour 750 → 655 ms median). The per-comment delivery check after the query (`deliveredQueuedCommentIds`) is most of that time. This change does not touch it. ## Risks - Low risk. Every predicate keeps the same logic. Only the probe shape and the evaluation order change. The benchmark compares each changed condition for every recovery action, including non-canonical saved run ids, and the complete results of both checks. - Previous-release story: no saved state, schema or identity changes. Holds saved by older releases are read with the same rules, so they carry forward unchanged. - Rows with the same comment `created_at` have no defined order, as before. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude Code with tool use (shell, file edits, local PostgreSQL). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 11:12:41 -06:00
DottaandClaude Opus 5.5	d82e5efeb9	perf(ui): cut repeated reads while a task is open (#20563) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - The board UI keeps an open task current with a shared company websocket and with polling fallbacks > - In a busy company, one open task sent 35 to 60 API requests in 17 seconds, and each request waits on the database > - Most of these requests were repeated reads: task summaries 22 times, the task run list 11 times, task browsers 6 times, and the 60 KB agent list 6 times > - The cause is not the open task. Other agents' run and task events invalidate company-wide lists on every 300 ms batch, and the task view polls runs and browsers on fixed intervals even while the websocket is open > - This pull request spaces company-wide refreshes, and it lets the websocket replace run and browser polling while it is connected > - The benefit is about 79% fewer reads from an open task in a busy company, with the same polling fallback when the connection is down ## Linked Issues or Issue Description Refs #17608 Refs #9627 **What happened?** An open task in a busy company sent the same reads again and again. In one 17-second visit, the UI requested `issues/summaries` 22 times, the task live runs 11 times, the task browsers 6 times, and the company agent list 6 times. The company live runs and the task's child lists (`parentId`, `createdFromIssueId`, `descendantOf`) were requested 2 to 3 times each. **Expected behavior** A busy company must not make an open task refetch company-wide lists on every event batch. While the live connection is open, the UI must use events, not fixed fast intervals, for task runs and browsers. The UI must keep its polling fallback when the connection is closed. **Steps to reproduce** 1. Open a task in a company where other agents run work. 2. Keep the task open for 17 seconds. 3. Count the API requests in the browser network panel. **Paperclip version or commit** Based on master at bd30ef8510. ## What Changed - `ui/src/lib/query-invalidation-batcher.ts`: Add a minimum spacing option to the invalidation batcher. A quiet lane flushes after the normal batch interval. A busy lane flushes at most once per spacing window. Add `createLaneRoutingBatcher`, which sends each invalidation to one of two batchers by query key. - `ui/src/context/LiveUpdatesProvider.tsx`: Route company-wide keys to a 5-second ambient lane. These keys are task lists and summaries, the agent list, heartbeats, company live runs, sidebar badges, the dashboard, costs and the company activity feed. All other keys, such as task detail, comments, task runs and browsers, keep the 300 ms lane. - `ui/src/lib/live-runs-cache.ts`: While the company connection is open, a successful active run list or active run polls every 15 seconds instead of every 1 or 3 seconds. Run lifecycle events already refresh these queries, and progress events patch them. - `ui/src/hooks/useTaskBrowsers.ts`: While the company connection is open, stop browser polling when no browser can change state. Keep the 3-second poll for a starting, running, idle or stopping browser, and when the connection is closed. The two callers pass the task's company. Socket open and reconnect already reconcile this active query. - `ui/src/lib/task-browsers-refresh.ts` and `LiveUpdatesProvider.tsx`: On `browser.*` activity for a task, refresh that task's browser list. If a read is in flight, one shared follow-up read runs after it settles, so an older empty result cannot stop polling. Two views of the same task share that follow-up. A list that no view observes becomes stale, so a returning view reads it. When the connection opens or resyncs, each browser list with a read in flight also gets one follow-up read, because missed activity is not replayed. - `doc/DATABASE.md`: Document the ambient lane and the new polling contract. - Tests: Add a fan-out test that replays a busy-company event stream for 17 seconds against an open task, plus unit tests for spacing, lane routing, key classification, the run interval and the browser interval. Update the recovery test for the connected active-run interval. ## Verification Request count over a fixed 17-second open window (`ui/src/context/LiveUpdatesProvider.fanout.test.ts`). The test mounts the reads that an open, running task keeps active. It replays a busy company: one run status event every second and one task activity event every 0.7 seconds, none for the open task. Fake timers make each run deterministic, so the spread is zero. The baseline used the same test with master's batcher, run interval and browser interval. | Read | Before | After | | --- | ---: | ---: | | Task summaries (sidebar) | 24 | 5 | | Company agent list | 17 | 5 | | Company live runs | 17 | 5 | | Child list: parent | 24 | 5 | | Child list: created from | 24 | 5 | | Child list: descendants | 24 | 5 | | Task live runs | 18 | 2 | | Task browsers | 6 | 1 | | **Total** | **154** | **33** | The baseline numbers match the staging capture well (summaries 22, browsers 6). - `pnpm exec vitest run src/context/LiveUpdatesProvider*.test.* src/lib/live-runs-cache.test.ts src/lib/query-invalidation-batcher.test.ts src/hooks/useTaskBrowsers.test.ts src/lib/task-browsers-refresh.test.ts src/hooks/useTaskPluginPanels.test.tsx src/components/task-side-panel/TaskSidePanel.test.tsx src/pages/IssueDetail.test.tsx` (in `ui/`): all pass. - `pnpm exec tsc --noEmit -p ui`: no errors in `ui/src`. - `pnpm check:token-gates`: clean. - Tests also prove these cases: - With the connection closed, task runs still poll every second and browsers every 3 seconds. - With a quiet company, one event refreshes the summaries and child lists after one normal batch. - `browser.started` on the open task refreshes its browsers. The same event on another task does not. - A browser that starts during a slow empty read appears after that read settles (`ui/src/lib/task-browsers-refresh.test.ts`). This test fails when the refresh joins the older read. - Two views and repeated events during one read cause one follow-up read. This test fails without the shared queue. - A list cached while the task was closed is read again when a view returns. - A connection that opens during an older empty browser read causes one more read, so a browser that started while the socket was closed appears. This test fails without the follow-up. - Task detail, comments, task runs, browsers, attention and another company's keys stay on the fast lane. - An unrecognized active result keeps the fallback interval. This is a local request-count proof. It does not include a timed browser journey on a deployed instance. ## Risks - Company-wide lists refresh at most once every 5 seconds from live events, so they can be up to 5 seconds late. After 5 quiet seconds, an event refreshes them in about 300 ms. Own mutations invalidate their queries directly, so they do not wait. - An active task run refreshes from events. Fields without an event, such as output silence, can be up to 15 seconds late while the connection is open. Reconnect still reconciles missed events. - A browser that appears without activity is not shown until the next activity or reconnect. Every browser lifecycle step logs activity on the task, so this case is not expected. - No server, schema or API change. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, with tool use and code execution in Claude Code. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 11:01:53 -06:00
DottaandClaude	84007892e9	refactor: move AGENTS.md section detail to docs and rules, add a bug-fixing section (#20585) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - `AGENTS.md` is the instruction file that each human and AI contributor reads before a change > - Pull request #20557 shortened the file, but several sections still held detail that applies to only some changes > - The scoped-rules section told agents to read each matching rule in full, and most changes match five rules > - The core engineering rules mixed three product invariants with process conventions > - This pull request moves that detail to the docs and to scoped rules, and adds a section on how to fix a bug > - The benefit is a 211-line file that states what applies to every change and points to the rest ## Linked Issues or Issue Description Refs #20557 **Issue type** Outdated or unclear contributor documentation. **Where is the issue?** `AGENTS.md` at the repository root, and `rules/`. **What's wrong?** - The scoped-rules section made agents read the full body of each matching rule before a change. The rule bodies total about 47 KB. - Sections 4, 6, 8, 9 and 10 repeated detail that belongs in `doc/DEVELOPING.md`, `doc/DATABASE.md`, a route rule, `DESIGN.md` and `CONTRIBUTING.md`. - Section 4 had a database reset command for `data/pglite`. That directory does not exist. - Section 5 had seven rules. Four of them were process conventions or path-specific detail. - The file did not say how to fix a bug. **Suggested fix** Make the rule headers the index. Move section detail to the document or rule that owns it. Keep only the three invariants in section 5. Add a bug-fixing section. ## What Changed - The scoped-rules section now tells agents to list the rule headers with one `grep` command. Agents read a rule body only for a design decision in its area, when the description is not sufficient, or when a reviewer cites it. - `rules/README.md` says that each `description` must state the required behavior in one sentence. - `rules/pull-request-review.mdc` has a description that states its requirements. - Section 4 (dev setup) and section 11 (pull requests) now point to `doc/DEVELOPING.md` and `CONTRIBUTING.md`. - The schema change workflow moved from section 6 to `doc/DATABASE.md`. - The API and auth expectations moved from section 8 to the new `rules/api-route-expectations.mdc`. - Section 9 links to `DESIGN.md` for design rules. `AGENTS.md` no longer tells contributors to run `pnpm check:token-gates`. - Added section 10, "Fixing a Bug": reproduce the error, write a failing test, write the fix, see the test pass, and verify the fix. - Section 5 now has three rules: company scope, contract synchronization, and the control-plane invariants. - The company-scope exceptions moved to the new `rules/company-scope-exceptions.mdc`. - Removed the strategic-docs rule. The plan-doc convention moved to the repo map. The artifact rule moved to section 7. - Removed rule 7. Five code comments that cited `AGENTS.md §5.7` now cite `rules/data-paths.mdc`. - Regenerated the SDK public source pin, because one of those comments is in `packages/shared/src/crash-points.ts`. - Added both new rules to `.greptile/files.json`. - The API route rule applies only to routes that read or write company data. Its status code list is a list of common codes. - The company-scope rule lists the sidebar company order as an instance-wide exception. - The `honeycomb-tracing` skill now points to `rules/data-paths.mdc` for the Telemetry workflow. ## Verification - Open `AGENTS.md` and confirm that each link resolves. A local script checked this. - Run `grep -E '^(description|globs|alwaysApply):' rules/*.mdc` and confirm that each rule prints a description. - Run `node tests/runner-e2e/source-sdk-public-inputs.mjs <HEAD> --check`. It passes locally. - `packages/shared/src/crash-points.test.ts` passed locally before the rebase onto `master`. - Five source files changed in comments only. No other test suite ran locally. ## Risks - An agent that reads only rule descriptions can miss a detail in a rule body. Reviewers still apply the full rules. - Pull requests and the definition of done are now sections 11 and 12. Sections 1 to 9 keep their numbers. - Dated plan documents under `doc/plans/` still cite `AGENTS.md §5.7`. They are historical records. - Pull request #20565 also changes `AGENTS.md`. The second one to merge needs a conflict fix in section 1 and section 2. ## Model Used - Claude (Anthropic), in Claude Code with tool use. - `claude-fable-5-2`. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [ ] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude <noreply@anthropic.com>	2026-11-10 11:00:31 -06:00
DottaandClaude Opus 5.5	765ccd8691	perf(chat): index chat-admission checks by company and payload issue id (#20562) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Chat connections save each external message as a `chat_actions` row before the server admits it as an agent wakeup. > - The server checks if an issue holds chat input that it did not admit. Recovery skips such an issue. Manual task start refuses it. > - On a hosted instance, the recovery read with this check used the most total database time: 488 calls at about 1 s each. The manual-start check ran 155 times at about 0.9 s. > - The check matches `chat_actions.payload->>'issueId'` against the issue. No index covers this value, so each call reads the full `chat_actions` table and its payloads. > - This pull request adds one concurrent partial index for the check. The check SQL does not change. > - The benefit is less background database load, so request reads wait less. The results stay the same. ## Linked Issues or Issue Description **What existing behavior does this improve?** The chat-admission check `unadmittedChatWakeupCondition`. Recovery uses it in the per-issue candidate read. Manual task start uses it in the held-input check. **Subsystem affected** Server chat admission, issue recovery, manual task start, and the database schema. **Current behavior** The check finds `inbound_wakeup` actions by `company_id` and `payload->>'issueId'`. Two nested checks find `failed_run_retry` actions and later `inbound_wakeup` actions on the same company and payload issue ID. `chat_actions` has no index on `company_id` or on the payload issue ID. Each call reads the full table and reads each payload. On a hosted instance, the two statements used about 630 s of database time in one statistics window. **Proposed behavior** The check and its nested checks read a small set of rows from one index. The admission result does not change. **Reason and benefit** The hosted database had many concurrent active queries. Request reads waited behind background work such as this check. **Breaking changes** None. The migration adds an index only. ## What Changed - Migration `0458_chat_admission_issue_index` builds `chat_actions_company_issue_kind_idx` with `CREATE INDEX CONCURRENTLY IF NOT EXISTS`. It runs through the existing top-level statement path, which repairs an invalid index on retry. - Keys: `(company_id, payload->>'issueId', kind, status)`. - Partial: `kind IN ('inbound_wakeup', 'failed_run_retry')`. - One index serves the outer input lookup, the failed-run retry lookup, and the later-input lookup. All three match on the same company and payload issue ID. - The Drizzle schema declares the index. The snapshot chain moves to `0458` and keeps five snapshots. - New regression test `server/src/__tests__/chat-admission-condition.test.ts` pins the admission semantics on real PostgreSQL: - Pending and failed input without a receipt holds the issue. Received, processed and cancelled input does not. Other action kinds do not. - A skipped receipt, a receipt for another agent, or a receipt in another company does not admit input. A failed or cancelled run still counts as admission. - The issue ID is compared as company-scoped text. Uppercase, array, null, other-issue and other-company values do not match. - Only an admitted retry in the same conversation and issue that lists the action releases skipped input. - Only later admitted input in the same conversation, issue and session generation releases a failed input. Pending input stays held. - The check reads `chat_actions` only through the new index. - `scripts/benchmark-chat-admission-index.ts` measures both caller statements with and without the index and fails if the rows differ. - `scripts/benchmark-chat-admission-index-migration.ts` times the migration through the normal migration runner. - `doc/DATABASE.md` documents the index and the benchmark commands. ## Verification Local SQL measurements on synthetic data. PostgreSQL 18.1 (embedded), default settings. The fixture has 100,995 `chat_actions` rows (662 MB): 60,000 GitHub actions with 6 KiB incompressible payloads, 2,000 issues with 20 admitted inbound messages each (3 KiB payloads), and 1,000 failed-run retries. Each case has 2 warmups and 9 samples of `EXPLAIN ANALYZE` execution time. Runs alternate: no index, index, no index, index. | Caller statement | Case | No index, median (range) | Index, median (range) | | --- | --- | --- | --- | | Manual-start held check | quiet issue | 3,093 ms (2,150–3,519) / 3,586 ms (2,375–11,235) | 0.036 ms (0.034–0.052) / 0.040 ms (0.033–0.047) | | Manual-start held check | admitted input | 3,555 ms (3,310–8,080) / 5,205 ms (3,353–9,525) | 0.049 ms / 0.052 ms | | Manual-start held check | unadmitted input | 3,002 ms (2,864–3,221) / 4,179 ms (3,200–6,585) | 0.051 ms / 0.044 ms | | Manual-start held check | failed, later admitted | 3,586 ms / 3,722 ms | 0.066 ms / 0.054 ms | | Manual-start held check | admitted retry | 2,733 ms / 4,953 ms | 0.049 ms / 0.053 ms | | Recovery candidate read | quiet issue | 43 ms (41–48) / 96 ms (44–219) | 0.047 ms / 0.055 ms | | Recovery candidate read | admitted input | 203 ms (48–575) / 174 ms (44–314) | 0.055 ms / 0.058 ms | | Recovery candidate read | unadmitted input | 66 ms / 144 ms | 0.053 ms / 0.054 ms | - Buffers per call fall from about 40,000 shared hits to 5–23. - Locally, the recovery read without the index uses a hashed full scan of `chat_actions`. The held check uses a full scan per call. On the hosted instance both took about 1 s per call. The local fixture is smaller than the hosted table. - Correctness: complete positional rows match across all four runs for all six cases (quiet, admitted, unadmitted, failed then admitted, retried, other-company decoy). The script asserts the expected held result for each case. - Migration timing: 600,001 `chat_actions` rows (1,759 MB), 300,000 of them in the index scope. First run through `applyPendingMigrations`: 4.2 s. Rerun after the history row is removed: 0.5 s. Concurrent build alone: 3.4 s. Index size: 30 MB. Commands: ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-chat-admission-index.ts OTHER_PAYLOAD_KIB=2 pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-chat-admission-index-migration.ts cd server && npx vitest run src/__tests__/chat-admission-condition.test.ts # 6 passed pnpm --filter @paperclipai/db check:migrations # passed pnpm --filter @paperclipai/server typecheck # passed ``` ## Risks - The migration builds one index concurrently. It does not block writes. On the 1.76 GB local fixture it took about 4 s. A larger hosted table takes longer, but the build does not lock out reads or writes. - Writes to `inbound_wakeup` and `failed_run_retry` actions maintain one more index. Status updates on these rows were already not HOT updates, because other partial indexes use `status`. - The planner has no expression statistics for a partial index. The new test pins that the check uses the index on an analyzed table with unrelated rows. - The check SQL does not change, so admission behavior does not change. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - Claude Opus 5.5 (Anthropic), model ID `claude-opus-5-5`, used through Claude Code with tool use and code execution. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 10:44:51 -06:00
DottaandClaude Opus 5.5	faaae003a9	perf(chat): find the conversation head from open delivery work (#20564) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - External chat messages go into a durable delivery queue. Each conversation drains in provider order. > - Each drain step reads the head of one conversation. The head query filters one endpoint's deliveries by state and thread. > - On a hosted instance, this query ran about 10,000 times at about 300 ms each. The database was busy, and request reads waited behind background work. > - PostgreSQL read every processed delivery of the endpoint and its `normalized_event` value to find a few open rows. > - This pull request finds the endpoint's open delivery IDs first and fetches only those rows. > - The benefit is less background database load. The selected head and the delivery order do not change. ## Linked Issues or Issue Description **What existing behavior does this improve?** The inbound conversation head query (`earliestOpenConversationDelivery`). **Subsystem affected** Server chat inbound delivery queue. **Current behavior** The query has `endpoint_id = $1 and (state in ('received', 'retry', 'processing') or (state = 'processed' and <pending inbound wake>))`, a thread filter on `normalized_event`, and a sort on `normalized_event` keys. No index matches the `or`. PostgreSQL scans all deliveries of the endpoint. For each row it reads `normalized_event` to test the thread. It also reads all of `chat_actions` to build the pending-wake set. A busy endpoint keeps all of its processed history, so the cost grows with that history. **Proposed behavior** The query selects `id in (<open delivery IDs of the endpoint>)`. That set is a `union all` of two small reads: - received, retry and processing deliveries of the endpoint, through the existing `chat_deliveries_work_idx`; - processed deliveries that an issued or processing `inbound_wakeup` action of the same endpoint (and company) still owns. PostgreSQL fetches only those rows by primary key, then applies the same reaction, thread and order rules. **Reason and benefit** The cost no longer grows with processed history. On a local fixture with 60,000 processed deliveries, the head query reads 1,309 shared buffers instead of 262,630. **Breaking changes** None. There is no schema change, migration, API change, timer or poll change. Related work: #17971 changed the pending-wake predicate of the same queue. #20400 added the index for the other chat delivery statement in the same report (`select state ... normalized_event->'githubAutomatic'->'context'->>'deliveryId'`). That statement already uses the #20400 index on master, so this pull request does not change it. ## What Changed - `delivery-ledger.ts`: add `openConversationDeliveryIds(endpointId)`. It returns the endpoint's open delivery IDs. It selects the same set as the old state predicate for that endpoint. - `conversation-queue.ts`: the conversation head query uses `id in (openConversationDeliveryIds(endpointId))` in place of the state `or`. The thread filter, reaction exclusion, order, limit and lifecycle dependency read do not change. - `inbound-queue-discovery.test.ts`: add a real PostgreSQL test. It compares the new set with the old predicate on three endpoints. It covers each state, issued and processing wakes, duplicate wakes, wakes of non-processed deliveries, processed, other-kind and null-delivery actions, an action on a different endpoint of the same company, and reactions. It also checks that the real captured head query returns the oracle's first row. - `benchmark-inbound-queue-discovery.ts`: add `--endpoint-history=<rows>` (a busy endpoint with 4 KiB payloads) and `--only=<fixture>`. Add a work budget: the treatment head query must visit at most 100 delivery rows on the history fixtures. - `doc/DATABASE.md`: describe the head query and the benchmark command. ## Verification Local SQL measurements. PostgreSQL 17.10 (Postgres.app, macOS arm64), disposable database, synthetic data, default settings with 256 MB shared buffers. The host was under heavy load from other work, so timings are noisy. Shared buffers and visited rows are stable. Each arm has two warmups and five alternating samples (median [min..max]). Baseline: `origin/master` at `8d2bf78323`. | Fixture | Query | Baseline | Treatment | Shared buffers | Delivery rows visited | Output | | --- | --- | ---: | ---: | ---: | ---: | --- | | 60,000 processed, 4 KiB | head | 290.09 ms [220.21..554.19] | 7.34 ms [5.85..7.68] | 262,630 → 1,309 | 60,002 → 4 | Equal | | 20,000 processed, 4 KiB | head | 276.02 ms [211.77..322.12] | 34.61 ms [4.45..194.15] | 67,618 → 486 | 20,002 → 4 | Equal | | 1,500 processed, 32 KiB | head | 15.88 ms [13.66..21.79] | 2.29 ms [1.64..7.75] | 10,602 → 80 | 1,502 → 4 | Equal | | 20 processed | head | 1.49 ms [0.92..3.66] | 1.85 ms [1.01..1.97] | 2 → 45 | 22 → 968 | Equal | - The deadline and ready selectors do not change. Their buffers are identical in both arms; their timings move only with host noise. - The small control is neutral. On a near-empty table, PostgreSQL picks a sequential scan for the open-state branch. This costs about 45 buffers. - The 60,000-row run passes `--require-work-budget`. The baseline exceeds the budget (`baselineExceedsWorkBudget: true`). This is the red/green proof. There is no timing threshold in CI. - On the treatment, the remaining head cost is the scan of `chat_actions` for pending wakes of the endpoint. The baseline also reads all of `chat_actions` for its hashed subplan. - `pnpm exec vitest run src/__tests__/inbound-queue-discovery.test.ts` (server): 6 tests pass, including the new equivalence test. - `chat-channels.integration.test.ts` filtered with `-t "reorder|orders|FIFO|conversation drain|lease renewal|receipt order|edit|lifecycle"`: 148 assembled chat tests pass. They cover Slack, Teams, Telegram, Discord and GitHub provider-order drains, head-of-line barriers, lease loss, lifecycle edits and wake retries. - `pnpm exec tsc --noEmit -p tsconfig.json` (server) passes. Reproduce: ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-inbound-queue-discovery.ts --baseline-ref=8d2bf78323 --endpoint-history=60000 --only=endpoint-history --require-work-budget ``` Set `PAPERCLIP_TEST_POSTGRES_ADMIN_URL` to use an existing disposable PostgreSQL server. The benchmark uses synthetic data only. ## Risks - Query plans depend on data and settings. These local numbers do not prove hosted request latency. A follow-up statistics window after deploy must confirm the gain. - The pending-wake branch still scans the endpoint's `chat_actions`. A partial index on pending `inbound_wakeup` actions would remove that scan. I did not add it, to avoid a migration. - Low behavior risk. The new set equals the old predicate for each endpoint, and the order expression is unchanged. Tests compare both on the same rows. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, with tool use (shell, file edit) in Claude Code. Extended reasoning was used. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 10:15:29 -06:00
DottaandClaude Opus 5.5	56aa160a4e	perf(native): index heartbeat runs by company and native session (#20560) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Native runs share a native session. Retention, recovery, resume and archive code reads all runs of one session from `heartbeat_runs`. > - On a hosted instance, the native retention lookup ran about 67,000 times in one day at about 22 ms, and about 10,000 times at about 11 ms in a later window. > - No index has `native_session_id`. Each read walks the agent's or the company's run history and filters the rows. > - This pull request adds one concurrent partial index on `(company_id, native_session_id)`. The SQL does not change. > - The benefit is less background database load. Request reads wait less, and the results stay the same. ## Linked Issues or Issue Description **What existing behavior does this improve?** The native session-run lookups. The largest caller is `sessionRetentionBlocker` in native harness backup and checkpoint retention. It selects `id, status, finished_at`, an incomplete-recovery flag and the issue ID for one company, agent and native session. **Subsystem affected** Server native runtime (retention, recovery, resume and archive reads) and the database schema. **Current behavior** `heartbeat_runs` has no index on `native_session_id`. PostgreSQL reads the whole run history of the company (or of the agent through `heartbeat_runs_company_agent_started_idx`) and filters by session. The cost grows with the run history, not with the size of the session. **Proposed behavior** The index finds the few runs of one session directly. Every caller already filters by `company_id` and `native_session_id`, so one index serves the agent-scoped and the issue-scoped reads. **Reason and benefit** This statement family used about 1,500 s of database time in one day on a busy hosted database. The local proof below shows 12.3 ms to 0.04 ms per call. ## What Changed - `packages/db`: add `heartbeat_runs_company_native_session_idx` on `(company_id, native_session_id) WHERE native_session_id IS NOT NULL`. Migration `0457_native_session_run_index` builds it with `CREATE INDEX CONCURRENTLY IF NOT EXISTS`. The migration is registered as a top-level-statement migration, the same way as 0454–0456. - Add a regression test in `native-harness-backup-expiration.test.ts`. It captures the real retention lookup and proves that its plan can use the index. It also pins the company and session scope: a live run of another company with the same session ID does not protect a checkpoint. A live run of the same agent in another session does not protect it. A live run of the same session does protect it. - Add `scripts/benchmark-native-session-run-index.ts`. It runs the real checkpoint retention pass (dry run), captures the exact SQL, and replays it with and without the index. It also times the migration through the normal migration runner. - `doc/DATABASE.md`: describe the index and the benchmark command. ## Verification Local SQL measurements, synthetic data. PostgreSQL 18.1 (embedded test server). Fixture: 100,000 runs (50,000 of the measured agent, 50,000 of a second agent), 4 runs per session, 4 KiB incompressible `runner_profile_json` per run, 638 MB table. Order: no index, index, no index, index. 15 `EXPLAIN (ANALYZE, BUFFERS)` samples after 3 warmups. | Pass | Plan | Median execution | Min / max | Shared buffers | | --- | --- | --- | --- | --- | | No index (1) | Seq Scan | 12.30 ms | 10.33 / 35.27 ms | 3,607 | | Index (2) | Index Scan using `heartbeat_runs_company_native_session_idx` | 0.036 ms | 0.021 / 0.115 ms | 38 | | No index (3) | Seq Scan | 12.38 ms | 10.24 / 26.14 ms | 3,607 | | Index (4) | Index Scan using `heartbeat_runs_company_native_session_idx` | 0.043 ms | 0.022 / 0.098 ms | 38 | - Correctness: the service SQL is the same in every pass. The returned rows (all columns) and the retention result are equal in every pass. The script fails on any difference. - Migration: the first run through the migration runner took 525 ms on the 638 MB fixture. The rerun took 273 ms and skipped the existing index. A direct concurrent build took 145–221 ms. Index size: 1.9 MB. - `pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-native-session-run-index.ts` - `npx vitest run src/__tests__/native-harness-backup-expiration.test.ts` (server): 108 passed. - `pnpm --filter @paperclipai/db check:migrations`: passed. Five snapshots remain. - `pnpm verify` exits 2 (a new script under `scripts/` is a global CI input). Required CI supplies the broad coverage. ## Risks - Low risk. The migration adds one index concurrently and does not lock writes. The SQL of every caller is unchanged. - The index adds a small write cost to `heartbeat_runs` inserts and to updates of `native_session_id`. Rows with a null session are not indexed. - Persisted run state: no saved run, session or checkpoint shape changes. State saved by the previous release carries forward unchanged. - Hosted latency is not measured yet. The numbers above are local SQL measurements. ## Model Used - Claude Opus 5.5 (Anthropic), model ID `claude-opus-5-5`, used through Claude Code with tool use (shell, file edits, local PostgreSQL). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 10:04:22 -06:00
DottaandClaude Opus 5.5	0b20ea6fe9	fix(accounting): keep budget admission and usage handoff alive under run-row updates (#20484) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Before a run starts provider work, Paperclip reserves its budget and binds a usage recorder. Both write the run's `heartbeat_runs` row. > - Run-log appends, output progress and lifecycle events update that same row while the run prepares and streams. > - #20385 fixed this race for the standalone usage-receipt write only. Budget admission and the recorder handoff still take a repeatable-read snapshot before they lock the run row. > - Each concurrent row update makes that snapshot stale. Four retries run out with SQLSTATE `40001`, and the run ends `adapter_failed` with raw SQL as its error. > - This pull request applies the #20385 pattern (READ COMMITTED under the existing locks) to those writers and to the final dispatch gate. It also gives exhausted retries a bounded cause. > - The benefit is that busy runs start and account normally, and a remaining failure names its cause. ## Linked Issues or Issue Description Refs #20385. Builds on #20483 (bounded failure cause and `withoutSqlStatementText`). **What happened?** The restart-chaos L1 workload with `--db-pressure 4` (harness writers that update each running run row, one row per statement, like a fast stream) failed on master. In one wave, 0 of 4 tasks passed. Every first run failed in `reserveRunBudget` before spawn. In an earlier wave, a run failed in `createRunUsageRecorder`. The stack in both cases is `could not serialize access due to concurrent update` (`40001`) on the run-row `FOR UPDATE`. The board `runError` showed the full `select ... from heartbeat_runs ... for update` statement. The server log line `heartbeat execution failed` dropped the database cause. Realism: the harness writers are synthetic, but the product has the same writers on the same row. `appendHeartbeatRunEvent` increments `next_event_seq`, output progress updates `last_output_*`, and lifecycle events land while a run prepares. On a hosted database the window between snapshot and row lock is wider than locally, so a busy run reaches the same race without the harness. **Expected behavior** Budget admission and the recorder handoff commit while other writers update the run row. Budget invariants stay intact: one reservation per run, a reached hard stop still refuses work, and committed holds count against later admissions. Usage receipts are journaled once. If retries still run out, the run shows a bounded cause without SQL, and the server log records the SQLSTATE. **Steps to reproduce** Run `server/src/services/run-accounting-contention.test.ts` against the parent commit. The deterministic cases commit a real `appendHeartbeatRunEvent` after the writer's transaction checks the company and before it locks the run. Six of the eight cases fail with `40001`. ## What Changed - `reserveRunBudget` runs at READ COMMITTED. All mutable reads follow the shared admission fences, the agent `FOR SHARE` lock and the run-row `FOR UPDATE`. Exposure stays one SQL statement (hold-to-ledger atomic). The `budget_reservations_run_idx` unique index and the run lock still prevent a second hold. - The final dispatch gate's accounting phase (`dispatchResolvedInteractionIfCurrent` through `withIssueThenRunLocks` in `run-dispatch/adapters/postgres.ts`) runs at READ COMMITTED. Its ownership phase already read the same staleness facts at READ COMMITTED under the same issue and run locks. Retry promotion and stale-run cancellation keep their repeatable-read snapshot. The first L1 proof wave found this writer exhausting `40001` once the other three were fixed. - `createRunUsageRecorder` runs its receipt-source handoff and its capture-failure fence at READ COMMITTED. Both lock the run row first, the same as `persistUsageReceipt` after #20385. - `withOperationAccountingTransaction` raises `AccountingContentionError` when retries run out. It has a bounded message, `code` keeps the SQLSTATE (`40001`/`40P01`), `cause` keeps the database error, and a warning logs both. - `failRun` shows that bounded message. The code stays `adapter_failed`, so chat and recovery retry paths still apply. #20483's `failureCause` records `40001`. All other SQL text handling comes from #20483 (`withoutSqlStatementText`), unchanged here. - `doc/DATABASE.md` documents the isolation choice and the failure contract. ### Inventory of REPEATABLE READ / SERIALIZABLE transactions that write run-scoped rows | Writer | Status | Notes | | --- | --- | --- | | `persistUsageReceipt` (`usage-receipts.ts`) | Fixed in #20385 | READ COMMITTED under the run lock. | | `reserveRunBudget` (`budget-reservations.ts`) | Fixed here | Seen in waves (`budget-reservations.ts:90`). | | `createRunUsageRecorder` handoff (`usage-receipts.ts`) | Fixed here | Seen in waves (`usage-receipts.ts:572`). | | `createRunUsageRecorder` capture-failure fence (`persistFailure`) | Fixed here | Same shape: run lock first, runs mid-stream. | | Native finalizer `claimCoordinator` (`native-run-finalizer.ts`) | Safe | A default READ COMMITTED transaction with `FOR UPDATE` on the coordinator row. It cannot raise `40001`. The wave errors there were `native_finalization_missing`, a symptom of the failed reservation (no coordinator existed yet). | | Final dispatch gate, accounting phase (`dispatchResolvedInteractionIfCurrent`) | Fixed here | Seen in proof wave `w-20261110T075857-s20386` (runs `140ddb10`, `c028c6c4`, `fea0ee5a`). Its ownership phase already used READ COMMITTED under the same locks with the same staleness reads. | | Retry promotion and stale-run cancellation (`promoteOrCancelDueRetry`, `cancelStaleQueuedRun`, same lock helper) | Follow-up | Kept at repeatable read: `loadGateFacts` combines wakes, comments, dependencies, tree holds and repair state in one decision. They act on queued or scheduled runs, not streaming ones. Not seen failing in waves. If retries run out, they now fail with the bounded cause. | | Run settlement `accountRunCost` (`run-cost-accounting.ts`) | Follow-up | Seen with `40001` in a wave log. Leaves the run pending; `reconcileRunCosts` retries it durably. Multi-aggregate (coordinator, receipts, images, closure). | | Tool cost events (`paperclip-runner-tool-authority.ts`, `costs.ts`) | Safe | Insert `cost_events` only; the run row is referenced, not locked or updated. | | Budget enforcement and evaluation (`budgets.ts`), billing reconciliation, accounting-integrity repair | Safe | Lock policy, invoice or company rows, not a streaming run row. Run reads are plain selects. | | Browser use, decisions, prompt-injection, fast responses | Safe | Write their own invocation/reservation rows, not `heartbeat_runs`. | | Read-only RR snapshots (`withAccountingReadSnapshot`, idle-sleep, tool gateway, customer success, `routes/decisions.ts`) | Safe | Read only, or no run-scoped writes. | ## Verification - Red on the parent commit, green on this branch: `server/src/services/run-accounting-contention.test.ts` (real embedded PostgreSQL). - `reserveRunBudget > reserves once when run events commit between its company check and its run lock` (red: `40001`) - `reserveRunBudget > reserves every run while back-to-back writers update the run row` (red: `40001`) - `reserveRunBudget > counts every committed hold, so successive admissions never exceed the budget` (red) - `reserveRunBudget > still refuses a run once the hard stop is reached` (red: `40001` instead of `409`) - `createRunUsageRecorder > binds its receipt source when run events commit between its company check and its run lock` (red: `40001`; green asserts the spooled receipt is journaled exactly once) - `createRunUsageRecorder > binds while back-to-back writers update the run row` (red: `40001`) - `reserveRunBudget > never creates a second reservation for one run when two dispatches race` (invariant; passes before and after) - `final dispatch gate > admits and hands off a reserved run when run events commit between its company check and its run lock` (red: `AccountingContentionError` after 4 × `40001`) - `createRunUsageRecorder > persists its capture-failure fence once when run events commit between its company check and its run lock` - `final dispatch gate > admits while back-to-back writers update the run row` (red: `40001`) - `exhausted retries > fail with a bounded, SQL-free cause that keeps the SQLSTATE` (new contract) - `run-completion.test.ts > saves a bounded cause and keeps the retryable generic code when accounting retries are exhausted` (saved code, message and `failureCause`, and log fields, through `failRun`) - Related suites pass: `usage-receipts-read`, `admission-independent-of-cleanup`, `budget-live-attempts`, `idle-accounting-work`, `budget-enforcement-scoping`, `closed-native-receipt-accounting`, `budget-evaluation-work`, `run-dispatch/adapters/postgres`, `heartbeat/run-completion` (all 126 run-completion cases pass; its `afterAll` embedded-PostgreSQL teardown exceeded 30 s on this loaded host, the known local flake). - `pnpm --filter @paperclipai/server typecheck` passes. - Latency of `reserveRunBudget` on the normal path (no contention, embedded PostgreSQL, 350 measured reservations per run, 3 runs each): before p50 14.7 / 15.0 / 18.6 ms, p95 25.6 / 31.4 / 39.4 ms; after p50 14.2 / 14.0 / 16.6 ms, p95 29.7 / 24.0 / 29.3 ms. No added latency: the statements are the same, only the isolation level changes. Under contention it removes the retry backoff. - Live restart-chaos L1 waves (`--seed 20386 --db-pressure 4`, codex and claude, K1): - Master before this change: `w-20261110T050818-s20386`, 0/4. Every first run failed in `reserveRunBudget` with `40001`. - Head `90530789b0` (first three writers fixed): `w-20261110T075857-s20386`, 2/4. Both codex tasks passed. Both claude failures (t02, t03) trace to the dispatch gate, now fixed. Those runs already showed the bounded cause, with no SQL on the board. The failure was logged with `sqlState` 40001. No `reserveRunBudget` or recorder `40001` remained. - Head `d5ed21926f` (dispatch gate fixed): `w-20261110T090531-s20386`. All 4 tasks reached done with no retry and R1–R6 passed. There were no failed runs and zero `40001` in the server log, under 310k pressure updates. Each task still failed the T-oracle `company_spend_settled` with `pending_runs=1`. That pending run is t02's continuation run `601ae80a`, cancelled before provider work as `issue_terminal_status`, whose accounting debt was not yet settled when graded about 15 s later. It is not a contention failure. Caveat: I edited the worktree during this wave (`worktree_changed_mid_wave`), so a clean wave on the final head follows. - Final head `9f1c480717`, clean worktree: `w-20261110T094417-s20386`. All 4 tasks reached done with no retry, and R1–R6 passed for each. There were no failed runs and zero serialization failures in the server log, under about 523k pressure updates. Each task still fails only the T-oracle `company_spend_settled` (`pending_runs=1`). It is the same cancelled pre-provider continuation run (`issue_terminal_status`), whose accounting debt was still unsettled at grading. That is a separate settlement-timing follow-up, not database contention. Master was 0/4 on the same seed. ## Risks - READ COMMITTED gives each statement its own snapshot. Admission reads policy, scope and exposure in separate statements. The shared company/project fences and the agent share lock exclude concurrent pause and policy edits, and exposure stays one statement, so each read is at least as fresh as the old snapshot. - Concurrent admissions of different runs stay best-effort, as `doc/SPEC-implementation.md` already states ("concurrent starts can exceed the same observed balance"). This change does not widen that window: each statement snapshot is newer than the old transaction snapshot. It does not add a company mutex. - A run that fails after exhausted retries now records `accounting_contention` instead of `adapter_failed`. Retry rules that key on `adapter_failed` spawn-like messages did not match this failure before, so no automatic retry changes. - No schema, migration or persisted-format change. ## Model Used - Claude Opus 5.5 (Anthropic), model ID `claude-opus-5-5`, used through Claude Code with shell, file-edit and code-execution tools. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-10 03:47:48 -06:00
DottaandPaperclip	0991d9bda1	fix(workspaces): protect migration sources and add guarded recovery service (#20443) ... ## Thinking Path > - Paperclip manages agents and their task workspaces. > - Online migration saves files before it publishes remote workspace authority. > - A saved migration journal can survive the importing process. > - Git cache expiration did not count that journal as a consumer. > - Expiration could remove a source and change its fingerprint while its import was incomplete. > - This PR protects unfinished imports and exposes a guarded internal service transition for an already affected cohort. > - New imports can preserve the current sources while all old recovery data stays retained. ## Linked Issues or Issue Description **What happened?** Git cache expiration could archive and remove a workspace after an import process ended but before its saved cohort finished. The saved source fingerprint then differed from the current archived workspace. Exact cohort resume correctly refused that changed source. Reopening the workspace cannot recreate the old metadata or fingerprint. **Expected behavior** An unfinished migration remains a durable consumer after process loss. If an older server already expired some sources, one canonical transition can fail the exact unpublished cohort without losing its snapshots, objects, source history, or recovery obligations. New attempts use the current verified sources. **Steps to reproduce** 1. Start a cohort import of eight Git worktrees with local changes. 2. Interrupt it after four snapshot uploads. 3. Let an older server expire two idle source worktrees. 4. Resume the saved cohort. It refuses the changed archived sources. Related: #20429 preserves exact cohort identity when independent companion imports change only the scope proof. #20424 preserves prepared recovery state for archived sources. This PR handles completed source expiration, not a scope-only change. Public searches found related expiration work and no matching compensation owner. ## What Changed - Count saved migration markers and unfinished migration journals as Git expiration consumers. Keep failed migration retention holds as consumers too. - Expose `supersedeExpiredRemoteWorkspaceMigrationCohort` as an internal service API for a privileged operator with a real database handle and reviewed company/cohort inputs. It is called directly by the PostgreSQL/Git test and reviewed one-time administrative qualification. It adds no CLI mode or HTTP route. The existing CLI still refuses a damaged cohort; this PR does not claim automatic CLI recovery. - Require an exact unpublished cohort of up to eight members. It requires completed expiration and an unexpired restore recipe for each missing member. The other members must retain their saved source fingerprints. - Recheck current source and recovery state under source, lifecycle, finalizer, and row locks. One transaction fails all old journals, writes audit records, and removes only their exact matched active markers. - Keep old cohort proofs, operations, snapshots, and object references. Genuine failure receipts use the existing failed-save retention hold. This transition does not report migration success. - Reuse the existing bounded source-lock queue when `sourceLockWaitMs` is set. Keep fast refusal by default. Cancellation targets only this waiter, and current checks still run after admission. - Record predecessor IDs on new attempts and reserve a snapshot generation above the existing ledger maximum. New success does not retire the old hold. - Document the owning transition and retention rules. ## Verification - The two new journal-consumer cases failed under the old expiration predicate and passed under the new predicate. - The full new recovery case passed in 21.12 seconds with real PostgreSQL locks, Git repositories, encrypted local object storage, and archive restores. It covers four retained uploads, two real expirations, unchanged old resume refusal, authority change refusal, transaction rollback, a held native finalizer, idempotence, eight new imports, dirty/untracked file restores, and a retention pass 30 days later with no object deletion. - Server TypeScript and module-boundary checks passed. - On `7cec8c915acfad2d08874eaf26abaa852f560219`, the queued-admission regression failed before forwarding the option (24.07 seconds), then passed (22.25 seconds). It verifies a real held project lock, cancellation that preserves the holder and all journals, release into full compensation, retention, and eight restored fresh imports. Current server TypeScript and module/diff checks passed. The only production follow-up changes are the optional queue input and its existing-owner call. - The earlier `737a0df3a71b10fe48d7bbfe7ffd8ae296b4852c` CI run had one Runner support failure: the unchanged credential-free Python/Pi calibration exceeded its outer 25-second subprocess deadline. That job passed 6,926 other tests and skipped four. The timeout is retained as a nonpass. The changed logical head requires fresh CI and review; no test deadline was raised. - The affected cohort, Git expiration, and eligibility suites passed all 148 cases in 228.41 seconds on `aa589f3f447e36d0277c32f8b44cbe5e84a673be`. Merged current master `a9d0946e64`; the only conflict retained both independent added test blocks. The complete merged cohort suite passed all 30 cases in 70.00 seconds on `737a0df3a71b10fe48d7bbfe7ffd8ae296b4852c`, including upstream larger-cohort controls. Final-head server TypeScript, incremental preflight, module-boundary, and diff checks passed. Unchanged expiration/eligibility evidence remains valid. Fresh `809ab704e619812d8f1bf38cf5de9c65893861cc` CI and review are pending. - On `809ab704e619812d8f1bf38cf5de9c65893861cc`, the complete recovery fixture passed in 21.38 seconds after adding one valid archived recipe with no restore point. It refuses with `migration_supersession_expiration_unverified` and keeps all workspaces, journals, and snapshots unchanged. The same case then verifies queue cancellation/release, full compensation, retained history, fresh imports, and restored bytes. Server TypeScript passed. This follow-up changes only the test and service-scope documentation; product bytes remain identical to qualified `7cec8c915acfad2d08874eaf26abaa852f560219`. - Earlier fixture attempts did not pass. They exposed the selection of a held source and an incorrect expected refusal string. The fixture now selects eligible sources and asserts the canonical authority refusal. Production guards were not relaxed. - Live qualification of the exact owning product bytes completed in 230.419 seconds. All eight old operations became failed with auditable supersession lineage. All eight old snapshot rows remained byte-for-byte identical, and their object references remain retained. The existing source-lock queue waited 1.151 seconds for a normal finalizer handoff. The three complete source/recovery passes took about 218 seconds including their transaction, which explains why the earlier 180-second total budget was insufficient for that measured workload. No source proof or publication guard was skipped. Compensation made no provider or object-storage calls. - Earlier live qualifications remain nonpasses: the 180-second attempt did not finish; its instrumented successor completed source checks and refused a busy source lock before mutation. The successful bounded-queue attempt retained those failure records. Fresh archived/online imports are a separate subsequent step and are not claimed complete here. - The local checks do not claim browser acceptance, app deployment, fleet enrollment, or a completed zero-downtime cutover. ## Risks - This owner mutates migration bookkeeping. It preserves all-or-nothing row comparisons and current source/recovery locks. A changed journal, authority, writer, finalizer, expired recipe, or partial transaction refuses the transition. - Historical snapshots and objects remain pinned after new success. This intentionally retains storage. Release requires a separate reviewed action. - An older importer cannot use the successor generation contract. Use the containing canonical owner for recovery. Normal app delivery must also carry the expiration guard; a private maintenance graph does not patch a running server's cleanup worker. - The migration owner crosses 1,000 lines. The bounded compensation transition remains beside its private source inspection, fingerprint, fence, reservation, and publication contracts. Moving it now would require exporting or duplicating those safety owners. No unrelated refactor or new framework is included. ## Model Used OpenAI GPT-6 through Codex, with reasoning, source editing, Git, and local execution tools. The exact serving model ID and context-window size are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-09 21:02:02 -06:00
Dotta	f73ff4ace9	fix(native): reprove stale filesystem preservation receipts (#20438) ... ## Thinking Path > - Paperclip manages agent work and preserves saved native sessions across releases. > - Filesystem independence receipts bind database facts to preserved controller and skill evidence. > - A workspace migration can add run metadata without changing those preserved bytes. > - That change makes the saved facts digest stale. Full native preservation then refuses the existing receipt, even after fresh source checks. > - WEB preservation already supports a full current proof and guarded receipt refresh. > - This pull request applies that pattern to full native receipts, reuses the authenticated archive, and keeps the existing ownership and destruction checks. > - The benefit is a current receipt without a new archive or provider replay. ## Linked Issues or Issue Description Refs: #20322. **What happened?** Adding the canonical `legacyWorkspaceRecoveryMigration` marker to a settled native run makes its saved receipt stale. The full native preservation owner checks current evidence but then refuses the old facts digest. **Expected behavior** The owner can refresh the proof metadata after it proves all current facts and preserved bindings again. Changed evidence or authority must leave the prior receipt intact. **Steps to reproduce** Use the added PostgreSQL regression. It saves a valid receipt for a succeeded source with 453 checkpoint parts, adds the producer-shaped migration marker, and calls preservation again. The unchanged owner fails with `native_harness_filesystem_independence_unverified`. ## What Changed - Reuse the prior controller archive through the existing authenticated readback path. - Require the old receipt to match every current immutable binding before a facts refresh. Reconstruct its exact digest from unchanged bindings and the prior proof fields. - Recheck current database facts, assets, controller and local files under the existing finalizer, selection, task and run fences. - Publish with an exact prior-receipt comparison. Keep a valid concurrent winner and refuse changed receipts or new owners. - Audit the prior receipt digest and four proof fields. Add focused source, integrity, race and DB-only validation tests, and update the database guide. ## Verification - Local Node24 canonical preflight and plugin SDK prerequisites passed. The Runner build came from the content cache. After a normal merge of fresh master, preflight confirmed unchanged build inputs. - Genuine RED on `3040448da5`: the saved receipt is valid before the migration marker and stale afterward. Reproof fails at the old receipt guard (one failed, 102 intentionally not selected). Both retained RED attempts reached that same guard. - GREEN on final local merge `00f4b5d678083106afc88fb2f7e0588961b46d6d`: 19 PostgreSQL controls passed, 91 intentionally not selected (17.75s). The wrapper completed cleanup. - The positive preserves the same archive, controller bytes, assets, local proof and all 453 checkpoint parts. It performs authenticated object reads and zero archive PUTs. Runs, results, finalizers and leases remain unchanged except for the receipt. The audit reconstructs the exact prior receipt. - DB-only validation passes with the original home, state directory and volume absent, while storage reads throw. - Refusal and race controls cover changed asset bindings, raw controller bytes, missing destruction evidence, unknown receipt fields, a valid concurrent winner, changed receipts and a late active owner. Existing WEB refresh, physical finalization-lock and saved-binding controls also pass. - Server TypeScript passed, including the adjacent integration test. Fresh Greptile is 5/5 on exact head `00f4b5d678083106afc88fb2f7e0588961b46d6d`, with no review threads ([review](https://github.com/paperclipai/paperclip/pull/20438#issuecomment-6756548830)). Final-head CI is terminal: 56 success, 4 skipped and 1 neutral. The aggregate `ci / verify` passed ([run](https://github.com/paperclipai/paperclip/actions/runs/42737704110)). - The first Runner-support job had one unrelated process-inspection nonpass: `server-stop.test.ts` expected a successful wrapper close, but its bounded process inspector returned no table. Its cause remains unknown. The unchanged test, process helpers, workflow and dependency inputs match the passed master control. One authorized same-head job retry passed all 328 files / 6,927 tests (4 skipped); the exact previously failed case passed in 665ms ([retry](https://github.com/paperclipai/paperclip/actions/runs/42737704110/job/129576420893)). No timeout, assertion or source change was made for the retry. ```sh node scripts/agent-preflight.mjs --skip-rust-debug pnpm --filter @paperclipai/plugin-sdk ensure-build-deps node --import ./cli/node_modules/tsx/dist/loader.mjs packages/db/src/test-postgres-command.ts pnpm exec vitest run server/src/services/native-runtime/native-harness-filesystem-independence.integration.test.ts -t "reproves stale native facts|retains stale native proof|guards stale native reproof|invalidates a published receipt after changed|actual physical-finalization lock|refreshes stale WEB facts|refuses a WEB facts refresh|retains or refuses the existing receipt when an earlier capture finishes late" pnpm --filter @paperclipai/server exec tsc --noEmit ``` ## Risks - Old receipt schemas and immutable bindings remain required. Full fresh proof carries compatible saved receipts forward; unknown fields or changed evidence refuse refresh and preserve the old receipt. - Full native preservation still requires canonical destroyed-provider receipts. The change retains the existing source capability, cancellation, finalizer and publication checks. - Only proof metadata changes. No provider operation, archive replacement, hosted recovery or deployment was performed for this PR. Live qualification remains with the operator after delivery. ## Model Used OpenAI GPT-6 (Codex), with tool use and code execution. The runtime does not expose a more specific model ID or context-window size. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge	2026-11-09 20:05:37 -06:00
DottaandPaperclip	3040448da5	fix(workspaces): refresh saved cohort source proofs on resume (#20429) ... ## Thinking Path > - Paperclip preserves agent work when a control-plane server is replaced. > - Online workspace imports save exact cohort, operation and snapshot identities for restart. > - A cohort proof also includes the complete current companion source scope. > - An independent companion import removes that companion from the local scope. > - The saved cohort then fails resume even when every saved member is unchanged. > - This pull request rechecks the current scope under fresh locks and refreshes its proof for all members in one transaction. > - The benefit is restartable online migration while independent work progresses. ## Linked Issues or Issue Description Refs: #19873, #20394, #20418. Related PR search found the original cohort owner, recovery-proof refresh and separate child-verification reuse. This fix addresses cohort scope freshness. **What happened?** An interrupted cohort rejects resume with `workspace_cohort_membership_changed` after a nonmember companion is migrated. The saved source proof includes companion workspace and task IDs. The exact saved members and their fingerprints can remain unchanged. **Expected behavior** The same saved cohort must resume after fresh admission. It must keep all member, operation and snapshot IDs. Changed members, active owners, changed journals and lost source locks must still refuse publication. **Steps to reproduce** 1. Start a two-member cohort and interrupt the second upload after the first archive is saved. 2. Import an archived nonmember companion through the existing canonical migration owner. 3. Resume the same two-member cohort. The original implementation refuses before it acquires the source fence. **Paperclip version or commit** Reproduced on master `3a5572c9e5`. **Deployment mode** Online administrative workspace migration with PostgreSQL and authenticated snapshot storage. ## What Changed - Admit a changed aggregate scope proof only when every saved member has a running journal and its current fingerprint matches both saved fingerprints. - Keep partial reservations on the original strict aggregate-proof path. Keep exact cohort and operation membership checks. - Run the existing source, lifecycle, recovery and finalizer admission before refresh. Lock member rows, inspect the current scope again, and compare every journal in one transaction. - Change only `cohortMigration.sourceProof`. Preserve all other metadata, identities, archive and recovery records. Abort the complete refresh on cancellation, a changed journal or a lost fence. - Extend the existing real PostgreSQL fixture with partial upload, canonical companion migration, refusal controls, transaction rollback, cold archive restore and replay. - Document the proof lifetime and resume boundary. ## Verification - Canonical Node24 worktree preflight passed. Plugin SDK build prerequisites passed. - Genuine RED on unchanged product: the real partial-upload and companion-import sequence fails with `workspace_cohort_membership_changed` (1 failed; 22 intentionally not selected; 10.44 seconds). - The identical positive passes after the fix (1 passed; 22 intentionally not selected; 9.87 seconds). - The complete focused cohort file passes: 23 tests in 33.33 seconds. Existing controls include changed member fingerprints, foreign and completed journals, active operations, peer cancellation, actual source-fence connection loss and outer-commit failure. - The new sequence also checks a held source lock, a held finalizer lock, cancellation before refresh, and an injected second-member update failure. The failed update rolls back every proof change. Both saved archives restore tracked and untracked work, and replay uses the same cohort. - After one final read-only preflight assertion, that complete new sequence passes again in 14.52 seconds with 22 existing cases intentionally not selected. Server TypeScript passes on the final files. Module boundaries and `git diff --check` pass. - Commands: `pnpm exec vitest run server/src/services/remote-workspace-cohort-migration.test.ts`; final case selection: `-t 'same uploaded cohort'`; `pnpm --filter @paperclipai/server exec tsc --noEmit`; `node scripts/check-module-boundaries.mjs`. - Initial local setup attempts remain nonpasses: sandbox PostgreSQL could not bind localhost, then the new archived companion fixture used a noncanonical repository folder. The corrected fixture uses the existing managed repository path. Neither setup failure is counted as the product RED. - Fresh [Greptile review](https://github.com/paperclipai/paperclip/pull/20429#issuecomment-6755862789) is 5/5 on exact head `6c640c4667b136e5416c1375f491729cf4bb9b49`, with zero inline threads. Required final-head CI is running. Hosted acceptance is not claimed by this PR. ## Risks - The old aggregate proof contains only a hash. Refresh therefore requires durable fingerprints for every saved member and repeats all current admission guards. A partially reserved cohort cannot use this path. - A stale proof must never hide a changed member or a new writer. Current source inspection, P/I/L/F locks, locked member rows, complete journal compare-and-swap and the existing capture and publication checks remain authoritative. - The all-member update must stay atomic. A database fault or cancellation rolls it back. The original cohort, operation and snapshot IDs remain fixed. - The change adds one bounded transaction only when a fully saved cohort's scope proof changes. It adds no recurring work, schema, provider, archive format, concurrency or deployment changes. ## Model Used OpenAI Codex, GPT-6 family, with repository tools and code execution. The runtime does not expose a more specific deployment identifier or context-window size. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes: #` / `Refs: #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-09 19:16:34 -06:00
DottaandClaude Opus 5.5	347d85fef3	perf(chat): index GitHub review lookups and share review-wait reads (#20400) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - GitHub chat endpoints let agents review pull requests. The server reads review state when it lists issues and when it updates GitHub checks. > - On a hosted instance, two GitHub review queries used the most total database time. One query ran about 660,000 times at about 33 ms. The other query ran about 10,000 times at about 1 s. > - The first query finds a source comment's chat link. No index covers `chat_message_links.comment_id`, so each call reads the full table. Issue lists also read the same review waits two times per request. > - The second query joins deliveries, links and runs on a JSON key. The planner walks the agent's run history in creation order and reads each run's context. > - This pull request adds four concurrent indexes, splits the run lookup into two small reads, and shares review-wait reads in one issue-list request. > - The benefit is less background database load, so request reads wait less. The results stay the same. ## Linked Issues or Issue Description **What existing behavior does this improve?** GitHub review state reads. These are the inherited review-wait lookup by source comment, and the review-check lookup of the run that a delivery's comment woke. **Subsystem affected** Server chat channels (GitHub review waits and checks), issue list attention maps, and the database schema. **Current behavior** - `readInheritedGitHubReviewWait` filters `chat_message_links` by `company_id`, `comment_id` and `direction`. No index has `comment_id`, so PostgreSQL reads the full table on each call. The run-origin check does the same lookup first. - An issue list calls the external review-wait read from the review attention map and again from the blocked-inbox attention map. The two maps read the same in-review issues. - `githubReviewCheckState` joins deliveries, links and runs with `context_snapshot->>'wakeCommentId' = comment_id::text`, sorts by `created_at desc` and takes one row. The planner reads the agent's runs in creation order and reads each run context. If no run matches yet, it reads all of them. The delivery filter on `normalized_event` and the link join on `delivery_id` also have no index. **Proposed behavior** The same rows come back from small index reads. Each issue's review wait is read one time per issue-list request. **Reason and benefit** These two statement families used about 33,000 s of database time in one cumulative statistics window. The database had about 50 concurrent active queries, and request reads waited behind this background work. **Breaking changes** None. The migration adds indexes only. ## What Changed - Migration `0456_chat_review_lookup_indexes` builds four indexes with `CREATE INDEX CONCURRENTLY IF NOT EXISTS`. It runs through the existing top-level statement path, which repairs an invalid index on retry: - `chat_message_links_company_comment_idx` on `(company_id, comment_id)` where `comment_id is not null`. - `chat_message_links_delivery_idx` on `(delivery_id)` where `delivery_id is not null`. - `chat_deliveries_github_automatic_delivery_idx` on `(endpoint_id, normalized_event->'githubAutomatic'->'context'->>'deliveryId')` where that value is not null. - `heartbeat_runs_company_wake_comment_idx` on `(company_id, context_snapshot->>'wakeCommentId')`. This index is not partial. The planner does not use expression statistics from a partial index. Without these statistics, it estimates many matches and keeps the creation-order walk. - `githubReviewCheckState` reads the delivery's comment IDs first. If there is a comment, it reads the newest same-agent run with one of these `wakeCommentId` values. If there is no comment, it skips the run read. The comparison stays text equality on `comment_id::text`. - `createExternalReviewWaitReader` shares one read per issue between the review and blocked-inbox attention maps of one issue-list request. The reader exists only for that request. - `doc/DATABASE.md` describes the indexes and the new read order. - `scripts/benchmark-review-lookup-indexes.ts` compares the pre-fix and new code with and without the indexes. `scripts/benchmark-review-lookup-index-migration.ts` times the migration on a large synthetic database. ## Verification Local SQL measurements on a synthetic fixture. They are not production timings. Environment: embedded PostgreSQL 18.1, baseline revision `02bfe71a6b`. Fixture: 50,000 links, 5,000 deliveries with about 2 KiB events, and 4,000 runs with about 12 KiB incompressible contexts. The wake run is in the middle of the run history. Each value is the median server execution time from `EXPLAIN ANALYZE` (2 warmups, 9 samples). The order was: no indexes, indexes, then no indexes again. | Caller and statement | Before (no indexes, two passes) | After | Shared buffers before → after | | --- | --- | --- | --- | | Inherited review wait, link by source comment (same SQL) | 2.72 / 2.36 ms | 0.076 ms | 929 → 12 | | Review check, wake run found | 31.9 / 21.9 ms | 0.29 ms (two statements) | 25,776 → 62 | | Review check, no wake run yet | 71.0 / 47.5 ms | 0.06 ms (two statements) | 34,861 → 12 | - Indexes alone do not fix the review check. The old SQL with the new indexes took 8.6 ms (run found) and 29.7 ms (no run), because it still walked the run history. The new SQL without the new indexes was neutral (23.5 and 35.1 ms). - Service wall times on this shared machine were noisy, so the table reports server execution time. - Correctness: the benchmark fails unless the inherited statement returns the same positional rows in each index state. The check service result and the final wake-run rows of the new code must also match the pre-fix module for both cases. - Migration timing, normal migration runner, synthetic data: 200,000 runs (1.8 GB with 8 KiB incompressible contexts), 500,000 links and 100,000 deliveries. First run 4.2 s; rerun 0.38 s. Separate builds: links by comment 1.5 s, run wake comment 1.1 s, deliveries 0.7 s, links by delivery 0.3 s. All indexes were valid. The run index was 8.3 MB. - New tests: - `server/src/__tests__/github-review-check-state.test.ts` checks that the newest same-agent run is selected. It also checks that other agents, other companies, uppercase IDs, non-string values, list-only `wakeCommentIds`, comment-less links and unknown deliveries do not match. It checks that the generated statements can use the new indexes. - `server/src/services/native-runtime/external-review-wait.test.ts` checks that the reader reads each issue one time, keeps concurrent callers correct, and rejects all waiting callers when a read fails. - Red/green: with the pre-fix `review-check-state.ts`, the behavior test passes and the index test fails. With this change, both pass. - Focused runs pass: `issue-blocker-attention`, `heartbeat-issue-liveness-escalation`, review-wait, review-check-state, external-review-wait, review-repair (106 tests), and `external-chat-wait.integration` (285 tests). `pnpm --filter @paperclipai/server typecheck` and `pnpm --filter @paperclipai/db check:migrations` pass. Commands: ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-review-lookup-indexes.ts --baseline-ref=02bfe71a6b pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-review-lookup-index-migration.ts ``` ## Risks - The migration builds four indexes concurrently. It does not block writes. On a large database, the run index reads every run context one time. The local run took 1.1 s for 1.8 GB from a warm cache. Cold storage on smaller compute can be slower. - The run index adds one entry for each run insert and for each run update that is not a heap-only update. Many runs have no `wakeCommentId`, so these entries hold a null key. - The review check now sends two statements instead of one when a delivery has a comment. Each statement reads only a few index entries. - When two matching runs have the same `created_at`, either can be selected. The previous query had the same tie behavior. - This change does not change the number of in-review issues that one issue list reads. The blocked-inbox map still reads all in-review issues of the company. A smaller scope needs a separate change to the liveness classifier. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`) by Anthropic, in Claude Code with tool use (shell, file edits, local PostgreSQL benchmarks). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-09 18:47:34 -06:00
DottaandClaude Opus 5.5	0116e45958	perf(db): index pending budget Stops instead of scanning all run results (#20391) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Budget enforcement stops agent runs when a budget hard limit is reached. The stop intent is saved in each run's `result_json` until run control delivers it. > - The budget worker, run control, and the idle-sleep check find these pending stops with a predicate on `result_json`. No index supports that predicate. > - Each check therefore reads every heartbeat run and its large result JSON from TOAST. On a hosted database, this statement family was among the most expensive: about 8,000 calls at about 1 s each, about 9,800 s in total. > - Pending stops are rare. The predicate is constant, so a partial index can contain only those rows. > - This pull request adds that partial index. The SQL that the server sends does not change. > - The benefit is that each check reads a few index entries instead of the full table. The database has more capacity for request work. ## Linked Issues or Issue Description **What existing behavior does this improve?** The check for committed budget Stops that are not delivered yet. The budget worker runs it each time it looks for work (`hasPendingBudgetEnforcement`), and again for each delivery pass (`listPendingBudgetCancellationScopes`). Run control and the idle-sleep check use the same predicate. **Subsystem affected** Budget enforcement in the server (`server/src/services/heartbeat/budget-cancellation.ts`, `server/src/services/budgets.ts`, `server/src/services/heartbeat/run-control.ts`, `server/src/services/idle-sleep-safety.ts`) and the `heartbeat_runs` schema in `packages/db`. **Current behavior** The query groups all rows of `heartbeat_runs` and reads `result_json->'startupCancellation'->'budgetEnforcement'` for each row. A limit of 1 does not help, because the group and sort occur before the limit. Cost grows with the run history, not with the number of pending stops. **Proposed behavior** A partial index, `heartbeat_runs_pending_budget_cancellation_idx`, contains only runs with a pending budget Stop. The planner uses it for all four callers. The results are the same. **Reason and benefit** Local SQL measurements show a 300x to 1,000x decrease in time and buffer reads (see Verification). **Breaking changes** None. ## What Changed - Added the partial index `heartbeat_runs_pending_budget_cancellation_idx` on `heartbeat_runs (company_id)`. Its predicate is identical to `pendingBudgetRunCancellationPredicate`. - Added migration `0455_pending_budget_cancellation_index.sql`. It uses `CREATE INDEX CONCURRENTLY IF NOT EXISTS`, and it is in the list of migrations that run outside a transaction, as `0436` is. - Moved the scoped run-control read and the idle-sleep check into exported builders in `budget-cancellation.ts`, next to the scope list query. The SQL does not change. The callers and the test now share the same statements. - Added a real PostgreSQL regression test. It checks that delivered, malformed, and missing intents are not pending. It also EXPLAINs the statements that the callers send (scope list with limit 1 and 100, scoped read, `EXISTS` check) and requires the new index in each plan. If a person changes a query shape, the server predicate, or the index predicate, the test fails. - Added `scripts/benchmark-budget-cancellation-scan.ts`. It captures the SQL that the real service sends, then compares the plans, timings, and complete rows with and without the index. - Updated `doc/DATABASE.md`. ## Verification Red/green regression test: - Before the migration, the new test failed: the plan was `Seq Scan` with the predicate as a filter. - After the migration: `npx vitest run src/services/heartbeat/budget-cancellation.test.ts` passes (17 tests). - Also passed: `src/__tests__/budgets-service.test.ts`, `src/__tests__/idle-sleep-diagnostics-postgres.test.ts`, `src/services/budget-resume-continuation.test.ts`. - `pnpm --filter @paperclipai/db check:migrations`, and typecheck of `@paperclipai/db` and `@paperclipai/server` pass. Performance and result equality (local SQL measurements only): ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-budget-cancellation-scan.ts --runs=20000 --payload-kib=16 [--reverse] ``` - Fixture: embedded PostgreSQL 18.1. 20,241 runs in 2 companies, with incompressible result JSON of about 16 KiB (table 379 MB). 40 pending stops in 6 scopes, 200 delivered or malformed decoys, and 1 cross-company intent. - The SQL is the same in both treatments. The script toggles only the new index. 2 warmups and 7 samples per query. Rows are compared outside the timed part. Ordered queries must match in order. The scoped run-control read has no `ORDER BY`, so it is compared as a multiset. | Query (caller) | Baseline median | With index median | Shared buffers | | --- | --- | --- | --- | | `listPendingBudgetCancellationScopes(db, 1)` (worker `hasPending`) | 688 ms | 2.1 ms | 243,500 → 1,158 | | `listPendingBudgetCancellationScopes(db)` (delivery) | 799 ms | 1.4 ms | 243,500 → 1,158 | | Scoped pending runs (run control) | 357 ms | 1.1 ms | 121,835 → 322 | | `EXISTS` pending (idle-sleep check) | 440 ms | 0.37 ms | 240,560 → 2 | - Reverse order (index first) gave the same result: 524 ms → 1.6 ms, 464 ms → 1.4 ms, 306 ms → 1.0 ms, 306 ms → 0.42 ms. - Plans change from `Seq Scan` (or a broad bitmap scan) to `Index Scan` or `Index Only Scan` on the new index. - All result rows are equal in every run. Migration duration: - 20,241 runs (379 MB): index build 2.0 s to 3.9 s. - 200,241 runs with 8 KiB result JSON (2.1 GB): index build 5.6 s. With this table size, the four queries change from 1,148 / 879 / 514 / 4,392 ms to 1.1 / 1.2 / 0.85 / 8.3 ms. - The build is concurrent, so it does not block run writes. ## Risks - Migration: the build reads every run's result JSON one time. It is concurrent and resumable (`IF NOT EXISTS`). The executor repairs an invalid concurrent index on retry. - Write cost: run writes evaluate the index predicate. The index contains very few rows, so the extra cost is small. - Predicate drift: if a later change edits only one of the two predicates, the planner cannot use the index. The new regression test detects this. - The hosted timings are not measured yet. The local numbers come from a synthetic fixture. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude Code with tool use (shell, file edits, local PostgreSQL). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-09 18:14:52 -06:00
DottaandClaude Opus 5.5	ab80fea62f	perf(recovery): probe run bindings per comment in the lost-wake check (#20412) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - The ownership reconciler finds user comments whose wake a restart lost, and it saves a wake for them (plan invariant 4) > - Its lost-wake check matched a task's runs with one OR across the legacy context ID and the native issue column > - With that OR, PostgreSQL can join runs only by company. It then tests each recent comment against every run of its company and reads each run's context > - On a hosted staging database, this statement used about 23 s per call on average (384 calls, about 8,900 s in total). One call ran for 35 s. Other requests waited behind it > - This pull request reads the check in three stages and probes the two run bindings separately with existing indexes > - The benefit is the same result with bounded, index-driven work for each recent comment ## Linked Issues or Issue Description **What happened?** The reconciler's user-comment lost-wake check was one of the most expensive statements on a hosted staging database. Query statistics showed 384 calls with a mean of about 23 s. One active call was seen at 35 s. The database compute was busy, and short authentication reads waited behind long statements. The statement matched runs with `(context_snapshot->>'issueId' = issue OR native_issue_id = issue)` in three subqueries. The OR gives PostgreSQL no join key except `company_id`. A local plan on synthetic data showed the cost: a hash join of 273 comments against all 38,002 runs, which took 1.0 s of a 1.3 s statement. The work grows with recent comments multiplied by the company's run count, and each test reads a run context. **Expected behavior** Each recent comment uses a small number of indexed probes. The check returns the same comments in the same order, with the same limit and grace logic. **Steps to reproduce** 1. Seed a company with a deep run history and a few hundred recent user comments. 2. Let some recent comments have no wake (for example, after a restart lost the wake of a steered comment). 3. Run the check. PostgreSQL can pick a hash join on `company_id` with the OR as a join filter. With nested loops off, the old statement takes seconds. The local benchmark below shows this. **Paperclip version or commit** Baseline: `02bfe71a6b`. **Deployment mode** Server with PostgreSQL. Local proof uses disposable PostgreSQL 18.1. Production and staging use hosted PostgreSQL. Related: the earlier change that split native and legacy bindings for other ownership reads (see the "Execution recovery query performance" section in `doc/DATABASE.md`). A search found no open pull request for this check. ## What Changed - `checkUserCommentsWithoutWake` reads in three materialized stages: 1. Recent user comments on assigned, non-conversation tasks that no wake request carries. This stage keeps the same issue, status and agent-closed rules. 2. Of those, comments with no live or later run and with at least one earlier run. 3. Of those, comments that no live run acknowledged in an item event (the steer check). Only this stage reads event payloads. - Each run lookup is two probes: one on the legacy context ID and one on the native issue column. Both use existing indexes. `exists (A or B)` becomes `exists (A) or exists (B)`, which is logically the same. - Each probe ends with `offset 0`. This keeps it a per-row index lookup. Without it, PostgreSQL can build a hashed subplan over all runs, or a hash join over all item events of the company. The repository already uses this fence in `execution-blocker.ts`. - The final `order by c.created_at limit N`, the projection, the grace window and the reported reason do not change. - Add `scripts/benchmark-comment-wake-check.ts`. It loads the check from an explicit baseline commit and from the working tree, and it compares the complete service result and the complete positional SQL rows before it records time. - Add a regression test for each run binding on its own: native only, legacy only, live run, later run, steered run, an acknowledgement before the comment, a log-only mention, a run that ended before the comment, and a run in another company. - Document the check and the benchmark command in `doc/DATABASE.md`. - No schema change, index, migration, or new startup work. ## Verification - `pnpm exec vitest run server/src/__tests__/ownership-reconciliation-report.test.ts --maxWorkers=1`: 34 passed. This includes the existing lost-wake, restart, steered and agent-closed tests and the new binding test. - `pnpm --filter @paperclipai/server typecheck`: passed. - `pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-comment-wake-check.ts --baseline-ref=02bfe71a6b --samples=7` Benchmark setup: PostgreSQL 18.1 (embedded, local), `shared_buffers` 128 MB, `work_mem` 4 MB. All data is synthetic, with md5-hex filler so contexts and payloads do not compress well. There are two companies per fixture. Two warmup rounds, then 7 timed samples for each arm, in alternating order. Each sample runs the real check function. Before any timing, each fixture asserts that the complete check result and every positional SQL row are equal for baseline and treatment, and that the fixture reports at least one owed comment. Every timed sample also asserts the same result. | Fixture | Runs / recent comments / owed | Baseline median | Treatment median | Speedup | Hash-join plan, baseline → treatment | | --- | --- | --- | --- | --- | --- | | small | 2,541 / 50 / 6 | 8.5 ms | 2.6 ms | 3.2x | 19 ms → 3 ms | | representative | 75,502 / 750 / 75 | 26.4 ms | 23.3 ms | 1.1x | 2,262 ms → 17 ms | | lost steer wakes | 38,002 / 750 / 75 | 454.7 ms | 66.9 ms | 6.8x | 2,717 ms → 68 ms | | deep history | 150,750 / 1,125 / 114 | 26.9 ms | 18.8 ms | 1.4x | 4,006 ms → 34 ms | | busy hour | 128,750 / 5,625 / 200 (limit) | 79.2 ms | 47.4 ms | 1.7x | 20,047 ms → 75 ms | | long steered runs (stress) | 19,100 / 600 / 60 | 626.4 ms | 457.4 ms | 1.4x | 5,871 ms → 502 ms | - The table above used baseline `02bfe71a6b`, the branch base at that time. After the rebase, a repeat run with baseline `8004ad069e` (the new merge base, with the helper guard fixed to run from the repository root) gave the same picture on a busier machine: small 15.4 → 9.1 ms, lost steer wakes 1,733 → 139 ms, busy hour 103 → 65 ms, all with equal results. - The "lost steer wakes" fixture shows the slow plan with default planner settings. PostgreSQL hashed all runs by company and tested 273 comments against 38,002 runs. - The last column runs each statement once with `enable_nestloop = off`. This makes the company-only hash join that the old statement allows visible, and it shows that the new statement has no such plan. The result is checked as equal in this mode too. Staging's 23 s mean matches this growth: recent comments multiplied by the company's run count. - Shared buffers fell in every fixture except "small" with default settings (for example, busy hour 176,416 → 89,803). - Neutral path: in the "long steered runs" stress fixture, every steered comment lost its wake. These comments correctly reach the steer check. That check must read the payload of each item event after the comment in the run that was live, so it is the remaining cost. In normal operation a comment sent to a live run has a deferred wake that carries it, so stage one removes it. ## Risks - Low risk. The predicate is the same conjunction of conditions. Only the evaluation order and the probe shape change, and the benchmark asserts complete-row equality on six fixtures and in both planner modes. - Rows with the same `created_at` have no defined order, as before. The benchmark uses distinct times so positional comparison is meaningful. - `offset 0` stops PostgreSQL from turning these probes into joins. If a task someday has a very large number of runs, each probe still uses the company and issue indexes. - Upgrade safety: this change reads saved run, wake and event state only. It changes no persisted shape, run identity, or saved session, so state saved by the previous release carries forward unchanged. A cutover test is not applicable. - Not verified on the hosted database. The local proof uses synthetic data, and I did not capture a hosted plan. Confirm with a fresh query statistics window after deployment. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, with tool use (shell, file editing, local PostgreSQL) in Claude Code. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-09 18:12:02 -06:00
DottaandClaude Opus 5.5	c985541a57	perf(db): index retry-exhaustion receipts for the attention scan (#20386) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - The attention feed shows runs that failed after automatic retries stopped > - To find these runs, the feed reads every `heartbeat_run_events` row of the company and filters the rows by a message prefix > - Run output makes this table very large, so each feed request does a large scan > - On a hosted test database, this one statement used the most total database time: 923 calls at a mean of 5 s (4,709 s in total) > - Request authentication waits behind this background work, so all users feel the load > - This pull request adds a small partial index that holds only the retry-exhaustion receipts > - The benefit is that the same query reads a few index entries instead of all company events ## Linked Issues or Issue Description **What existing behavior does this improve?** The attention feed query that finds retry-exhausted runs (`listAttentionExhaustedRuns`). **Subsystem affected** Server attention feed and the `heartbeat_run_events` table schema. **Current behavior** The query reads all company rows in `heartbeat_run_events`, filters them by `event_type = 'lifecycle'` and the `Bounded retry exhausted` message prefix, and then joins the few matches to failed or timed-out runs. The cost grows with all run output. It does not grow with the number of exhausted runs. **Proposed behavior** A partial index holds only the matching receipts. The query plan reads the index and joins a few rows. The query text and the result do not change. **Reason and benefit** The scan was the most expensive statement by total time on a loaded hosted database. A local reproduction shows a 54x faster query and about 116x fewer buffer reads. **Breaking changes** None. The API, the feed rows, and their order do not change. ## What Changed - Add the partial index `heartbeat_run_events_retry_exhausted_idx` on `(company_id, run_id, id DESC)`. The index covers only rows where `event_type = 'lifecycle'` and `message like 'Bounded retry exhausted%'`. - Add migration `0454`. It uses `CREATE INDEX CONCURRENTLY IF NOT EXISTS`. The migration runner runs it as a top-level statement, the same as migrations 0432, 0436 and 0450. - Add a regression test. It pins the row order (newest run first, then the newest receipt on a tie) and the latest receipt per run. It also checks that the query plan can use the new index. If the query predicate changes so that the index no longer applies, the test fails. - Add `scripts/benchmark-exhausted-run-attention.ts`. It measures the same query with and without the index, and the time to build the index. - Document the index in `doc/DATABASE.md`. ## Verification Cause and thesis. The scan cost comes from reading all company events, not from the few exhausted runs. Thesis: an index that holds only the receipts makes the query cost depend on the number of receipts, and keeps the result identical. The benchmark below confirms the thesis. Rejected alternative without a migration. I first tried a LATERAL lookup that starts from the failed and timed-out runs. On the same fixture it was about 2x slower (median 379 ms against 194 ms). It reads the full event history of each failed run with random I/O, and that costs more than one sequential scan. Local SQL benchmark (the SQL that the service generates; same SQL with and without the index): ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-exhausted-run-attention.ts --runs=30000 --events-per-run=100 --samples=9 ``` Fixture (synthetic): one company with 30,000 runs (3,819 failed or timed out) and 3.0 M events, plus a decoy company with 0.5 M events. The table is 1.4 GB. About 5% of events are `lifecycle` events. Events of 20 concurrent runs are interleaved. 1 in 23 runs has a receipt, some runs have two receipts, and output decoys contain the prefix. Two agents are terminated. Embedded PostgreSQL 18.1 on an Apple laptop. The hosted database is Neon with different compute, so the absolute times are local SQL measurements only. The script runs two cycles (without index, then with index; then with index, then without index) to expose cache bias. Each measurement has 2 warmups and 9 samples. | Query | Without index | With index | Samples and spread | Output check | | --- | --- | --- | --- | --- | | `listAttentionExhaustedRuns` | median 157 ms (96–1,271 ms) | median 3.3 ms (2.2–5.7 ms) | 18 each | 133 rows, positional rows equal in all 4 measurements | | Buffers (EXPLAIN ANALYZE) | 127,743 blocks | 5,580 blocks | | plan uses the new index (asserted) | Speedup: 48x (median), on head `ae6037b2a0` (the same SQL and index as the final head). The machine was under heavy load from other work, so the spread without the index is wide. An earlier run on the first head gave 248 ms against 4.6 ms (54x). Index build (`CREATE INDEX CONCURRENTLY` from the migration file): 1.7 s and 2.5 s for the 1.4 GB table. Index size: 152 KiB. Review fix: the query now writes `event_type = 'lifecycle'` as a SQL literal, not a bound parameter. With prepared statements, PostgreSQL can reuse a generic plan. A generic plan cannot prove that a bound parameter matches the index predicate, so it would not use the index. Tests: - `cd server && npx vitest run src/__tests__/attention-service.test.ts`: 44 passed. The new test checks a fresh plan and a forced generic plan (`plan_cache_mode = force_generic_plan` with `PREPARE`). It failed with the bound `event_type` parameter and with a changed message prefix (confirmed red), and it passes with the fix. Locally, the file's `afterAll` database cleanup hook timed out on a heavily loaded machine (load average about 28). The timeout also occurs when the new test is excluded. - `pnpm --filter @paperclipai/db check:migrations`: passed. - `pnpm --filter @paperclipai/db typecheck` and `pnpm --filter @paperclipai/server typecheck`: passed. - `pnpm verify`: see the CI results for this head. ## Risks - Migration time. A concurrent index build reads the full `heartbeat_run_events` table and does not block writes. Locally, the build took 1.2–2.5 s for 1.4 GB. The time grows linearly with the table size. I did not time the build on a production-size clone. On a database with a 5 s full company scan, I estimate the build at tens of seconds, which is in the 1–2 minute budget. This estimate is not proven. - If the build stops, PostgreSQL can leave an invalid index. The migration runner repairs invalid concurrent indexes when it runs again, and `IF NOT EXISTS` makes a rerun safe. - The index predicate must stay textually equal to the query predicate. If someone changes the message prefix or binds a predicate value as a parameter, the planner cannot use the index. The new test catches both cases, for fresh and generic plans. - Each new receipt writes one more small index entry. Receipts are rare, so the write cost is very small. - The hosted improvement is not verified until deployment. After deployment, compare a new query-statistics window for this statement. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude Code with tool use (shell, file edits, local PostgreSQL). Standard context window and reasoning mode. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-09 17:37:20 -06:00
DottaandClaude Opus 5.5	c57cd1bdb9	perf(server): read plugin lifecycle inbox heads in one pass (#20405) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Plugins get agent, project and agent runtime changes from the `resource_lifecycle_events` journal. Each plugin acknowledges events one resource at a time. > - The inbox page query checked each unacknowledged event against all older events of the same resource. Each check walked the acknowledged history of that resource. > - Agent runtime streams get a new event for each configuration change, so one resource can have thousands of acknowledged events. The cost grew as pending events times acknowledged history. > - On a hosted instance, three copies of this read ran for 601 seconds each, and one earlier copy ran for 19 minutes. The delivery worker runs it again after each acknowledgment. > - This pull request selects the head of each resource in one pass and keeps the same result. > - The benefit is that the page read is linear in the company journal size. In local tests it is 250x to 660x faster, and the result rows are equal. ## Linked Issues or Issue Description **What happened?** The plugin lifecycle inbox page query (`select "id", "company_id", "resource_type", "resource_id", "action", "created_at" from "resource_lifecycle_events" where ...`) ran for 601 seconds on a hosted database. Three copies were active at the same time. **Expected behavior** A lifecycle page read must stay fast when a resource has a long acknowledged history and a pending backlog. **Steps to reproduce** 1. Give a company 40 agents with 1,500 `agent_runtime` events each. 2. Acknowledge the first 1,200 events of each agent for one plugin. 3. Call `pluginLifecycleInbox(db, pluginId).list(companyId, 100, undefined, ["agent", "project", "agent_runtime"])`. 4. The read takes about 10 seconds for 60,000 events of that company. At 200,000 events it takes about 6 minutes. **Paperclip version or commit** `02bfe71a6b` (master). **Deployment mode** Hosted (PostgreSQL). Local repro uses embedded PostgreSQL 18. ## What Changed - `server/src/services/plugin-lifecycle-inbox.ts`: `list` now selects one head per resource with `DISTINCT ON (resource_type, resource_id)`. The head is the unacknowledged creation, else the oldest unacknowledged event. Then the query applies `afterId`, id order and the limit. This is the same set that the old `firstForResource` predicate admits. `acknowledge` keeps the old predicate for its single-event check. - `plugin-lifecycle-inbox.ts`: new `hasPending(companyId, types)`. It returns whether any unacknowledged event exists. Each resource with an unacknowledged event has a head, so this gives the same answer as `list(companyId, 1).length > 0`. - `server/src/services/plugin-lifecycle-delivery.ts`: the idle-sleep journal check uses `hasPending`. This keeps its early exit. A one-row `list` page would read the full journal. - `server/src/__tests__/resource-lifecycle-events.test.ts`: new database test for heads across acknowledged history, a creation recorded after transitions, acknowledged gaps, shared ids across resource types, per-plugin progress, another company, `afterId` pages, limits, `hasPending`, and the next head after an acknowledgment. The test also passes on the old query, so it locks the contract. - `scripts/benchmark-plugin-lifecycle-inbox.ts`: new benchmark. It loads the baseline service from git, runs both on the same fixture, alternates order, asserts equal rows, and prints plans. - `doc/DATABASE.md`: describes the read cost and the benchmark command. - No schema change, index or migration. ## Verification Thesis: the old read cost is (unacknowledged candidates) x (acknowledged older events per resource), because each candidate walks the acknowledged prefix of its resource. One pass that keeps the per-resource head removes that product and returns equal rows. Baseline plan at 220,080 events: 40,020 candidates each walked about 3,999 older rows, which gave 160,039,980 acknowledgment probes and 562,140,833 buffer hits. The treatment plan reads the journal once with a hash anti join and sorts the 40,020 unacknowledged rows (3,925 buffer hits). Local SQL timings (embedded PostgreSQL 18, Apple Silicon; event counts include a 20,000-event second company, synthetic data, warm cache, one warmup, order alternates): | Fixture (events / acknowledged) | Case | Before median | After median | Samples (after) | Speedup | | --- | --- | --- | --- | --- | --- | | 40,060 / 16,040 | page of 100, all types | 3,263 ms | 13.1 ms | 3 (12.0-14.1) | 250x | | 80,080 / 48,060 | page of 100, all types | 10,137 ms | 23.9 ms | 5 (22.7-32.6) | 424x | | 220,080 / 160,060 | page of 100, all types | 355,718 ms | 538 ms | 3 (72-785) | 662x | | 1,020,080 / 960,060 | page of 100, all types | not run (est. > 30 min) | 1,682 ms | 7 (1,203-2,384) | - | | 80,080 / 48,060 | page of 100, agent and project only | 1.5 ms | 1.6 ms | 5 | neutral | | 80,080 / 48,060 | idle-sleep check | 14.5 ms | 13.8 ms | 5 | neutral | | 1,020,080 / 960,060 | idle-sleep check | not run | 406 ms | 7 | - | - Result rows are equal (`assert.deepEqual` on all mapped rows, in order) for each case where both versions ran. - The agent runtime revision read in `plugin-agent-runtime-state.ts` and `agent-file-store.ts` (`select id ... order by id desc limit 1`) uses a backward index-only scan and reads 5 buffers at 1M events. It is not changed. Commands: ```sh pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-plugin-lifecycle-inbox.ts --baseline-ref=02bfe71a6b --agents=40 --per-agent=1500 --acked=1200 --samples=5 pnpm --filter @paperclipai/server exec tsx ../scripts/benchmark-plugin-lifecycle-inbox.ts --baseline-ref=02bfe71a6b --agents=40 --per-agent=25000 --acked=24000 --samples=7 --treatment-only cd server && npx vitest run src/__tests__/resource-lifecycle-events.test.ts src/__tests__/plugin-lifecycle-delivery.test.ts src/__tests__/agent-runtime-hooks.test.ts ``` - `resource-lifecycle-events.test.ts`: 28 passed. `plugin-lifecycle-delivery.test.ts`: 40 passed (includes idle-sleep "none" and "present"). `agent-runtime-hooks.test.ts`: 22 passed. - `tsc --noEmit -p server`: pass. ## Risks - The page read is still linear in the company journal size, because acknowledgments are per plugin and the journal has no retention yet. At 1M events a page takes about 1.7 s locally. Each acknowledgment wakes another full pass. A per-plugin cursor or retention can remove this later. - The planner can choose a different plan on the hosted database. The local plans use a hash anti join and one sort. The hosted improvement is not yet measured. - `acknowledge` still checks one event against older events of its resource. That check is linear in that resource's history per call, as before. - Low behavior risk: the new test passes on both the old and new queries. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude Code with tool use (shell, file edits, local PostgreSQL). Extended reasoning on. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-09 17:37:14 -06:00
DottaandPaperclip	199670ba99	fix(accounting): prevent usage receipt stalls during streamed run updates (#20385) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Native Runner commits usage receipts before it acknowledges retained events. > - Usage receipts and streamed run logs update the same run row. > - A repeatable-read snapshot can become stale before the receipt writer locks that row. > - Continuous log writes can exhaust all accounting retries and stall the retained event. > - This pull request uses the existing run lock with READ COMMITTED for standalone receipt writes. > - Other accounting operations keep their consistent snapshot. Stall diagnostics retain safe nested error codes. ## Linked Issues or Issue Description Related: #20235. **What happened?** A hosted native run stopped on a retained usage event. Its diagnostic reported `Error at source seq N`. The saved outbox and accounting records locate the failing delivery boundary. Traces show repeated accounting transactions while streamed events still updated the run row. The historical inner exception is unavailable. A controlled PostgreSQL reproduction proves a matching defect: a run-log append after company validation makes the receipt writer's repeatable-read snapshot stale. Repeated appends exhaust all four retries with SQLSTATE `40001`. This is a demonstrated failure mechanism; attribution of the historical incident remains an inference. **Expected behavior** Commit the receipt under its existing run-row lock despite concurrent run-log writes. Observe concurrent finalization and preserve late-receipt debt. Keep duplicate receipts idempotent and reject conflicting or cross-company receipts. **Steps to reproduce** Run `server/src/services/usage-receipts-read.test.ts`. The concurrency regression uses real PostgreSQL and the production run-log append function. It commits a log append after company validation and before the receipt locks the run. Before the repair, the receipt rejects with a wrapped `40001` after four attempts. After the repair, it commits once. The finalization variant verifies that a newly settled run receives late-receipt debt without replacing settled state. ## What Changed - Allow aggregate-lock-protected accounting writers to select READ COMMITTED. Keep repeatable read as the default. - Use READ COMMITTED only for standalone usage receipt writes. Keep the existing run lock, immutable receipt journal, replay checks and transactional budget-work publication. - Add PostgreSQL regressions for concurrent log appends, concurrent finalization, duplicate delivery and the unchanged default snapshot. - Read the outer event-commit error and at most three nested causes for an existing safe error code. Exclude exception messages and SQL. - Document receipt isolation and bounded stall diagnostics. ## Verification - Red: the production receipt writer exhausted four retries with PostgreSQL `40001` under controlled concurrent run-log appends. - Red: wrapped database and transport stall diagnostics returned `Error` instead of `40001` and `ECONNRESET`. - Green: Runner control-plane tests passed all 207 cases. All 68 server assertions passed across receipt reads, native usage delivery and cost accounting. Cost-accounting teardown exceeded its 30-second limit twice on this loaded host, after all 28 assertions passed. The workspace project retained its configured 30-second hook limit despite the CLI override. This is a local suite cleanup failure, not a passing suite; the same revision passed the complete server suites in CI. - Server layered TypeScript checking passed, including source and test layers. Runner TypeScript checking passed. Server checks cover `ccfe3bdeb1ab88537a03fd6af9044f66863939a5`; the unchanged Runner checks cover its parent. - Local environment: macOS arm64, Node 26.4.0, disposable embedded PostgreSQL. Native usage-delivery tests use the real Rust receiver. - CI at `ccfe3bdeb1ab88537a03fd6af9044f66863939a5`: [build](https://github.com/paperclipai/paperclip/actions/runs/42714760702/job/129493568428), [typecheck](https://github.com/paperclipai/paperclip/actions/runs/42714760702/job/129493568367), native Runner integration, browser shards and all nine serialized server groups passed. All 12 general server shards passed in the [full run](https://github.com/paperclipai/paperclip/actions/runs/42714760702). Final rollup: 59 successful checks/statuses, three intentionally skipped checks, no pending or failed checks. - [Greptile reviewed this revision at 5/5 with no actionable findings](https://github.com/paperclipai/paperclip/pull/20385#issuecomment-6753163397). - Hosted evidence came from the task, run, saved sandbox outbox, accounting receipts and traces. The run started fresh and did not cross a deployment. No original agent turn was replayed. - The hosted repair has not been deployed. The original task has not been resumed. A fixed-revision remote-provider user journey remains unverified. ## Risks - READ COMMITTED changes snapshot timing for standalone receipt writes. The run-row lock protects all mutable receipt/accounting reads and serializes competing receipts and finalization. Other accounting operations retain repeatable read. - Receipt identity, replay conflict checks, company scoping, budget publication, retry bounds and acknowledgement rules remain intact. - No persisted format, provider identity or database schema changes. Existing saved state needs no migration. - Diagnostics inspect at most four objects and retain only the existing identifier format, with an 80-character code limit. - The reproduced race matches the incident boundary and timing, but the original inner exception was not recorded. Rollout and live acceptance remain necessary before incident resolution. ## Model Used - OpenAI Codex, GPT-6 family, with code and shell tools. The exact model ID and context window are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-09 17:35:13 -06:00
Dotta	0eacad0d0c	fix: refresh preserved harness receipt facts without copying archives (#20322) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Volume-free deployment must preserve historical controller files before removing the old disk. > - A WEB preservation receipt binds an archive and source files to the selected session and database facts. > - Later metadata changes can make those facts stale while the preserved files and archive remain unchanged. > - The existing owner refuses every stale receipt, so preservation cannot converge. > - This pull request refreshes only facts freshness after it verifies the same source bytes, checkpoints and archive. > - Existing locks and an old-receipt digest comparison prevent a concurrent replacement from being overwritten. ## Linked Issues or Issue Description Refs #19814 for WEB evidence preservation without settling remote recovery. Refs #19832 for bounded larger inventories. Related harness receipt PRs were searched; no existing change provides this guarded refresh. **What happened?** A valid WEB preservation receipt becomes stale after later run metadata changes. Its original-volume owner refuses another preservation attempt because an invalid receipt already exists. This leaves an eligibility blocker even when the source and saved archive are unchanged. **Expected behavior** The original-volume owner can refresh stale facts only after it proves every other persisted binding unchanged. It retains the prior receipt and remote recovery state. **Steps to reproduce** 1. Preserve a settled session's WEB files and controller evidence. 2. Add later run metadata so its database facts digest changes. 3. Preserve the same scope again. The previous implementation refuses at the existing-receipt check. **Paperclip version or commit** The failure was reproduced on master `12523fb677585fcd6da929f868014514a4e96e87`. This branch includes master `1b7fe33432016b3b27ccdfbf7b8944da4b40726d`. **Deployment mode** Managed Linux server with PostgreSQL and durable object storage. ## What Changed - Reuse the exact prior archive for existing WEB receipts. Recheck current source bytes, controller history, checkpoint material and archive bindings. Read back ciphertext and verify its size and hash. - Permit only database/local-observation freshness changes. Selected session, source run, controller, archive, WEB entries, and assets must still match the prior proof. Local inode and timestamp observations may change across attempts; preserved bytes, paths and modes must match. - Recheck current facts and source files under the existing finalizer, task and run fences. Accept a matching concurrent winner or require the exact previous receipt digest before replacement. - Retain the prior database and local facts digests, witness fingerprint, observation time and receipt digest in the same company-scoped activity transaction. Require those four fields to reconstruct the exact prior proof from unchanged current bindings before replacement. Normal audit redaction stays enabled. - Preserve current-key checks and archive reads on ordinary idempotent calls. Keep active-source, changed-evidence and cancellation refusals. - Document the refresh contract. No schema, saved-run format or public API change. ## Verification - Genuine RED: the new real PostgreSQL/encrypted-archive case failed at the old previous-invalid gate. - Before the audit review follow-up, the full local owner suite passed **94/94 integration cases in 50.01 seconds**. It covers same-archive refresh with no PUT, audit history, current-key failures, unreadable archives, cancellation, changed files, replaced volume, active sources, matching concurrent winners and conflicting receipt replacement. - The cases also cover a source becoming active during an idempotent readback. Earlier 91- and 93-case runs preceded these final review guards and are not the final result. - Server typecheck, module boundaries and diff checks passed on the final production/test bytes before the clean master merge. Required CI supplies final-head breadth. Four narrow post-merge refresh/current-key/idempotent regressions passed in 5.70 seconds on `82e270f29fff98442c4184b96082f72f18a88721`. - The fixtures use a real disposable PostgreSQL database and actual local encrypted archives/storage. Controlled faults affect the stated storage or concurrency boundary. They do not prove a hosted refresh or archive plaintext cold restore. - The existing integration file now exceeds 1,000 lines. Keeping these cases with its private original-volume, controller, archive and PostgreSQL fixture avoids duplicating that setup. - Initial worktree preflight stalled on the global package-manager wrapper. Preflight completed with the existing pinned toolchain. No setup failure is counted as a product test pass. - Review found that activity redaction could change a full prior-receipt copy. A new regression enabled the real username censor and reproduced that mismatch. The fix stores only the four changed scalar fields and their original proof digest; a prepublication canonical reconstruction guard rejects dropped or unknown fields. - On the audit follow-up, 16 affected real PostgreSQL cases passed in 11.98 seconds; 80 unchanged cases were intentionally skipped. They include real redaction with a username-containing WEB path, reconstruction across two refreshes, unknown prior fields, CAS, active sources, current-key failures, unavailable archives and cancellation. Final server typecheck and boundaries passed. This was an intermediate revision; the final-head results appear below. - A second review found that comparing old inode/timestamp observations also broke ordinary valid retries. Three real cases reproduced valid-receipt touch/inode failures and stale-facts touch failure. The fix permits metadata freshness changes across attempts while keeping exact byte/path/mode/checkpoint/archive coverage and the existing locked within-attempt metadata fence. - Final local owner suite on the metadata follow-up: **102/102 integration cases passed in 44.04 seconds**, including valid touch/new-inode retries, stale refresh with the same archive and no PUT, four-scalar audit reconstruction, changed bytes/mode/entries, and a touch during archive readback that must refuse. Server typecheck, module boundaries and diff checks passed. The final-head CI and review results appear below. - Final head `c81475c927d0862dcb8d2c2356dc41ab4a27e63f`: [PR workflow attempt 5](https://github.com/paperclipai/paperclip/actions/runs/42667287803/attempts/5) completed successfully at 19:24:28 UTC on 2026-11-09. All 51 jobs are accounted for: 49 passed and 2 were skipped. The actual [final ci / verify](https://github.com/paperclipai/paperclip/actions/runs/42667287803/job/129382061558) and [E2E aggregate](https://github.com/paperclipai/paperclip/actions/runs/42667287803/job/129381486342) passed. Typecheck, build and the selected test lanes passed. The exact-head rollup is successful with no pending or failed checks. - Attempt 5 resolved both trusted workflows to `3a2f71db31aa99633610dc241f55f34ac65124de`, after #20339 merged. Its routing gate passed and real jobs started. This verifies successful startup and completion of this rerun; it does not exercise the empty-runner fallback because routing succeeded. - Earlier CI failures on `82e270f29fff98442c4184b96082f72f18a88721` and attempts 1–4 of this final-head workflow remain nonpasses. Attempt 1 had interrupted leaf jobs and failed aggregates. Attempts 2 and 3 ended in workflow failure without a final verify job. Attempt 4 failed startup with zero jobs and empty-runner errors. Those failures are not counted as passes or labeled unrelated. - [Greptile](https://github.com/paperclipai/paperclip/pull/20322#issuecomment-6746395090) and [Ponytail](https://github.com/paperclipai/paperclip/pull/20322#issuecomment-6746327827) reviewed the unchanged final head at **5/5**. Both historical review threads are resolved; no inline thread remains open. - Hosted application to an actual stale scope remains pending normal release delivery. ## Risks - Refresh must not bless different preservation evidence. The unchanged-binding checks, fresh file and checkpoint proof, exact archive reuse, source capability and locked receipt comparison remain mandatory. - A fresh capability has a new witness fingerprint and expiry. The audit retains the old fingerprint, database/local facts digests and observation time. All unchanged proof bindings remain on the current receipt. Their canonical reconstruction must match the old digest. The new capability is validated at entry and publication. - Readback verifies ciphertext size/hash and current-key checkpoint material. This change does not claim a new archive GCM/plaintext restore. - Archive identity and rows remain unchanged, so retention ownership does not change. Failed refreshes retain the previous receipt, original files and unresolved remote recovery obligations. - Older receipt shapes are not rewritten automatically. Normal validation and named preservation refusals remain in force. ## Model Used OpenAI Codex, GPT-6.1 Sol (`gpt-6.1-sol`), with reasoning, repository tools and code execution. Context-window size is not exposed by the runtime. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge	2026-11-09 13:26:27 -06:00
DottaandPaperclip	4d5265fe7e	Preserve fully covered historical workspace sources (#19872) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Workspace migration must preserve local files while retaining unfinished recovery obligations. > - A shared Git source needs proof for its companion workspaces before import can publish. > - Recovery backfill can add a historical-source marker to an exhausted prepared-export hold. > - The hold owner rejected that marker even when every recorded allocation already belonged to its proven prepared source. > - This pull request accepts only that fully validated form through the existing source owners and publication fences. > - Unrelated work can continue while import saves the local files and keeps the remote recovery hold intact. ## Linked Issues or Issue Description Refs #19830. No separate public issue was found. A search for the marker found no open duplicate PR. **What happened?** A companion workspace with an exhausted prepared-export hold blocked the whole shared Git cohort after canonical recovery backfill added its historical-source marker. The prepared and historical source readers both accepted the same allocation. **Expected behavior** Local file preservation can proceed when all historical references are already covered by the proven prepared source. The recovery hold and remote obligations remain unchanged. Unknown or uncovered sources stay blocked. **Steps to reproduce** 1. Create a shared Git repository with a selected leaf and a companion workspace. 2. Give the companion a settled failed export, accepted result, exhausted recovery and blocked task. 3. Run canonical historical recovery backfill for its retained allocation. 4. Import the selected leaf through the normal online migration owner. **Paperclip version or commit** Reproduced on `4185e308659abf0887930e20049ca6e7cbfc0e81`. **Deployment mode** A source installation with legacy local Git workspaces and object storage. ## What Changed - Validate the exact historical marker schema, run and unique lease references against the already proven prepared source and declared allocations. - Reuse the canonical historical-source inspector and compare the same provider allocation and remote working directory. - Reject unknown fields, malformed markers and foreign, duplicate or uncovered references. - Keep the full marker in the existing hold fingerprint and retain the existing source, task, lifecycle, finalizer and publication checks. - Add real PostgreSQL/Git tests through shared-cohort inspection and the encrypted import/restore owners. ## Verification - The unchanged owner failed the actual selected-leaf importer regression with `online_workspace_source_scope_unproven`. The canonical prepared/historical reader controls passed before that refusal. - Production head `3e678e10fa` passed 41 focused PostgreSQL/Git cases across three files in 18.93 seconds after rebasing onto the new finalizer schema migration. This includes 14 new cases; 80 unrelated cases were filtered out. The final test-only review update passed both additional multi-allocation controls plus the original selected-leaf cold restore (3/3, 11.29 seconds); TypeScript passed again. - The positive uses the actual historical backfill producer. It cold-restores an encrypted selected-leaf snapshot with the original Git tree unavailable and keeps the peer's task, finalizer, result, allocation and recovery action unchanged. - The tests retain an unrelated active object-backed run, prove the peer finalizer lock is held, refuse bad bindings and reject late marker changes without discarding the uploaded snapshot. - Server TypeScript, module-boundary checks and `git diff --check` passed. The canonical PostgreSQL wrapper exited and cleaned up. - Final-head CI passed: 56 successful checks and four intentional skips, with no failures or pending jobs ([run](https://github.com/paperclipai/paperclip/actions/runs/42397090541)). Greptile reviewed `0cbf0a0255` at 5/5 with no open findings; GitHub reports CLEAN/MERGEABLE. ## Risks - The allowance applies only to the existing exhausted prepared-export hold. Other recovery forms and unknown or uncovered references remain blockers. - A marked hold adds database reads proportional to its already declared allocations during maintenance inspection. It adds no provider calls, payload download or recurring background work. - Import saves the current local files. It does not claim that unsaved remote files were recovered, that a provider stopped or that execution may resume. Existing holds and warnings remain authoritative. - Local tests use the real encryption and restore owners with a local object backend. Hosted backfill and normal-delivery qualification remain separate. ## Model Used OpenAI Codex, based on GPT-6, with reasoning, repository tools and code execution. The exact serving snapshot and context-window limit are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-07 11:53:00 -06:00
DottaandPaperclip	4185e30865	Recover archived commits from original bare sources (#19855) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Workspace migration must preserve saved files before the web server releases its local volume. > - An archived Git checkout can retain a trusted branch-deletion receipt after its private clone and generated project cache are removed. > - The original repository can still exist at its recorded file URL, but the archive owner did not check that source. > - This pull request permits a narrow, verified original bare-repository source for the exact recorded commit. > - The existing encrypted snapshot and publication owners then preserve the workspace through their normal migration path. ## Linked Issues or Issue Description No public issue exists. Searches for the archived-source error and original bare Git source found no duplicate change. **What happened?** Migration reported `archived_git_source_unavailable` for an archived checkout even though its original bare repository still contained the exact saved commit. The private clone and generated cache were absent. **Expected behavior** The canonical owner can use the recorded original local repository when its full commit identity and source ownership are proven. Uncertain or changed sources remain blocked. **Steps to reproduce** 1. Create an isolated checkout from a local bare repository. 2. Close it through the normal cleanup owner and retain the successful branch-deletion receipt. 3. Remove the private clone and generated cache, while retaining the recorded original repository and full base revision. 4. Inspect the archived workspace for migration. **Paperclip version or commit** Reproduced on `84908d176b2800f4c792c4249c610ec0baebdd28`. **Deployment mode** A source installation with existing local Git workspaces and shared object storage. ## What Changed - Consider the exact configured file-URL repository only after the canonical primary source is definitively absent. - Require a matching source record and successful cleanup receipt, the exact full base/deleted commit, a contained bare SHA-1 repository, bounded standard configuration and alias-free metadata. - Restrict this source path to local Git transport and a minimal environment. Reconstruct the tree only in private migration scratch. - Retain existing source fingerprints, journal identity, encrypted upload/readback and final publication checks. Lock and recheck the configured source and cleanup record before publication. - Add real PostgreSQL/Git coverage for encrypted cold restore, lost-reply retry and refused source or publication changes. ## Verification - The unchanged owner failed the real four-object original-source regression with an ineligible inventory. - The review regressions failed before each repair: four returned-primary retry/publication cases and two actual production metadata/reaper cases. - Final head `8925519310` passed all 40 focused PostgreSQL/Git tests in 56.38 seconds. Four positive formats use canonical/legacy metadata and ordinary/verified-tip cleanup. Each imports an encrypted snapshot, removes the original file URI from reach, then authenticates and cold-restores exact files, executable mode and Git history. - The same file covers source/receipt/writer guards, changed sources before publication, authenticated lost-reply reuse and 18 returned-primary directory/alias/unreadable cases. Refused publication retains returned edits and uploaded ciphertext. - Server TypeScript, module-boundary checks and `git diff --check` passed on this revision. Canonical test wrappers exited and cleaned up. - An earlier focused run also passed 22 existing archived-Git/restore-point controls. `pnpm verify --explain` completed without executing extra suites. Required CI supplies final broad coverage. - Final head passed all 60 CI/review contexts: 56 successful checks and four expected skips. Greptile reviewed this exact head at 5/5, with no open review threads. - One unchanged archive segment-boundary test timed out on both framework attempts in the initial server shard. The one job-only retry passed with unchanged code and timeout. The test and its resolved local import graph match a green control revision. The original failures remain retained; the cause is unresolved. ## Risks - The fallback is intentionally narrow. Original repositories with a different full tip, unsupported configuration, aliases (including an aliased instance root), external object storage or more than 10,000 metadata entries remain blocked. - The first source check and final publication check add bounded local filesystem and Git work to this maintenance path. They add no recurring worker or network Git access. - Original repository files remain intact. Importing a retained workspace does not make its configured local file URL portable for future fresh project work. That separate configuration dependency still requires preservation and qualification before volume removal. - The local regression uses the real encryption and restore owners with a local object-storage backend. It does not claim a hosted backfill or a deployed migration. ## Model Used OpenAI Codex, based on GPT-6, with reasoning, repository tools and code execution. The exact serving snapshot and context-window limit are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-07 11:05:25 -06:00
DottaandPaperclip	b8e02fc2b4	fix(native): preserve bounded larger web inventories (#19832) ... ## Thinking Path > - Paperclip manages AI agents and preserves their work across server changes. > - Native harness preservation stores retained web-server files in authenticated archives. > - A retained skill can contain hundreds of valid local files. > - The WEB evidence owner rejected any directory or inventory above 128 entries. > - This blocked preservation of two 462-file skills even though their payload fit the existing byte limits. > - This pull request shares finite inventory bounds between capture and archive validation. > - It preserves every file and keeps the execution, identity, writer, and publication guards. ## Linked Issues or Issue Description Refs: #19814 **What happened?** WEB evidence preservation rejected a retained source with 927 local skill files. The source had settled execution ownership. The files fit the existing payload limits. The directory enumeration failed before archive publication because its entry limit was 128. **Expected behavior** Preserve a valid finite inventory within explicit file, payload, path, and metadata limits. Keep remote recovery obligations unchanged. **Steps to reproduce** 1. Retain two 462-file skills and one three-file skill under a settled native source. 2. Request canonical WEB evidence preservation. 3. The old owner rejects directory enumeration. The added integration test reproduces this refusal with real files and PostgreSQL. ## What Changed - Share the WEB limit through the existing controller archive owner: 10,000 total entries, 4 MiB of manifest metadata, and 4,096 bytes per path. - Apply the limits to filesystem capture, published binding validation, and archive descriptor validation. - Keep the existing 16 MiB per-file and 64 MiB payload bounds. Keep authority history at 128 entries and 32 epochs. - Add real archive and cold-restore coverage for 927 files, legacy manifest compatibility, and bound refusals. Document the limits. ## Verification - Genuine baseline RED: the new 927-file integration case reaches the original `captureWebEvidence.directoryNames` limit and fails before publication. - The initial setup attempt failed before test collection because the generated plugin SDK was absent. The required SDK build fixed setup; it was not counted as a regression result. - The first affected three-suite run passed 93 cases. The large roundtrip exceeded the generic 15-second case deadline. That failure is retained. The isolated large case passed with a 60-second case limit, but full CI later exceeded that limit while the other 4,577 tests in its shard passed. Both timeout failures are retained. The final fixture keeps all 927 files and 18.5 MB, uses bounded 16-way independent comparisons, and has a 120-second whole-case limit. The canonical preservation signal remains 60 seconds. No production deadline or assertion changed. - The 927-file case then passed: encrypted archive, authenticated cold restore, all bytes/hashes/modes, unchanged remote leases, and database-only validation with source volume absent and storage reads forbidden. - The final metadata repair adds a genuine RED case: an entry list below 4 MiB previously emitted a larger complete manifest without rejection. The owner now checks the complete serialized manifest. All ten focused cases passed after that repair. The final bounded-I/O fixture passed the same ten cases in 37.26 seconds, including the full 927-file roundtrip. All 93 other affected cases passed in the preceding three-suite run. Fresh required CI supplies broad final-head coverage. - Server TypeScript, module boundaries, and whitespace checks pass. Run the focused PostgreSQL checks from `server/` with the repository wrapper: ```sh node ../cli/node_modules/tsx/dist/cli.mjs ../packages/db/src/test-postgres-command.ts -- node ../node_modules/vitest/vitest.mjs run src/services/native-runtime/native-harness-filesystem-independence.integration.test.ts --testNamePattern 'preserves all 927|existing 128-entry WEB|WEB manifest beyond|oversized WEB filesystem' --hookTimeout 90000 --maxWorkers 1 --fsModuleCache ``` ## Risks The owner can hold more entries in memory. The fixed 64 MiB payload, 4 MiB metadata, path, and entry bounds constrain that cost. The archive format and old receipt bytes do not change. Older builds still have the 128-entry limit and cannot qualify a larger new receipt. This change does not settle remote recovery, grant execution authority, alter finalizer locks, or change publication CAS rules. No hosted preservation or deployment was performed for this PR. ## Model Used OpenAI `gpt-6.1-sol`, with code execution and repository tools. The context window size is not exposed. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes: #` / `Refs: #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-07 09:11:00 -06:00
DottaandPaperclip	ae1f781cac	fix(native): preserve web files without settling remote recovery (#19814) ... ## Thinking Path > - Paperclip manages work that AI agents perform for users. > - Native sessions retain files on the web server and state in a remote provider. > - Replacing the web server must preserve its files without changing remote recovery authority. > - The existing maintenance owner requires destroyed-provider receipts even when all web writers have settled. > - This can keep the old web volume required only because a remote recovery obligation remains unresolved. > - This pull request adds a closed web-byte evidence mode to the existing preservation owner. > - The benefit is durable web-file coverage with unchanged remote references, failures and continuation policy. ## Linked Issues or Issue Description Refs #19748, #19806. A search for native harness filesystem evidence and open web/harness changes found no duplicate implementation. **What happened?** A settled successful native source can retain a raw controller, a separate warm supervisor and provider-home files while its historical external lease has no termination receipt. The existing filesystem-independence owner refuses before it can preserve these web files. One retained skill file can also remain physically present after its version row was deleted. **Expected behavior** Preserve every nonexcluded web file as authenticated evidence. Keep missing files absent and deleted skill versions deleted. Leave VM references, recovery actions, failures and execution authority unchanged. Validate the published web-byte receipt on an empty replacement using database bindings only. **Steps to reproduce** Use the included successful-source fixture with a settled web owner, an unresolved external lease, real controller/supervisor files and a retained skill whose version row is deleted. The baseline rejects at its destroyed-provider guard. The new explicit maintenance mode preserves the files and validates on a replacement. A separate fixture uses a prior successful source, a failed retained last run, a genuinely absent controller, a warm supervisor and 267 durable checkpoint parts. **Paperclip version/commit** Baseline `384fa2b7be`; final branch rebased onto `585c885168`. Current head: `990210d7e9`. **Deployment mode** Original-volume maintenance followed by an ephemeral replacement. No hosted operation or provider request is part of this PR. ## What Changed - Add explicit `web_evidence` maintenance mode and a separate `paperclip.native-harness-web-evidence.v1` receipt. Keep the existing terminated-provider mode and old manifest shapes. - Archive the closed canonical session-root inventory, the separate warm supervisor and exact admitted skill manifests through the existing encrypted `original_volume_source_evidence` owner. Preserve bytes and modes. Keep canonical credential exclusions. - Preserve local skill edits and deleted-version files as forensic evidence. Create no skill version, executable checkpoint, provider backup or recovery authority. - Require original-volume capability, settled web writers, physical/finalizer locks, exact task/source/cohort/input bindings and final byte/mode/membership comparisons. Keep genuinely absent raw controllers absent. - Bind allocation and stamp identity while allowing later external status and cleanup observations. Validate replacements from durable database and archive bindings without the original anchor, filesystem or storage reads. ## Verification - Node 24.22.2, PostgreSQL 18.1, macOS arm64. The unchanged baseline fails at the real destroyed-provider guard. The final revision passes all 85 owner, original-volume capability and unchanged continuation-policy cases in 21.14 seconds. - Tests perform real encryption, persistence through the S3 storage interface backed by the owned local fixture, authenticated restore and exact byte/mode comparisons. The 281-byte file remains present while its version row remains absent. The evidence archive stays separate from the provider-session backup scope. - The supervisor-only case preserves 267 database checkpoint parts, keeps the raw controller absent and validates without original-volume identity. Existing strict-mode and old receipt controls pass. - Negative controls cover active web writers, expired but owned finalizers, physical owners, foreign controller/supervisor identities, missing manifests, symlinks, changed bytes/modes/membership/source during upload, changed durable bindings, incomplete receipt coverage and invalid late publication. Concurrent attempts retain one valid winner and one audit event. - Server TypeScript, module boundaries, diff checks and private-data scans pass. The verification planner's first invocation used a wrong script path; its canonical invocation refused a plan because fixture inputs changed during selection. Neither attempt counts as a pass. Required CI will provide broader application coverage. - Earlier fixture and treatment failures remain recorded. They exposed a missing helper, JSONB property-order instability, missing separate-supervisor mode coverage and fixture timing/source/count errors. The final same owner suite passes without weakened assertions. - A canonical cleanup audit found two additional observation fields: the cleanup controller and manual-attempt ID. Their real publication updates reproduced false receipt invalidation on the first PR head. The narrow correction keeps WEB coverage valid through those observations while changed allocation identity still fails. The exact same 85-case suite passes afterward. The final `990210d7e9` head has fresh Greptile 5/5 with no comments or unresolved threads. Required CI run [42370607882](https://github.com/paperclipai/paperclip/actions/runs/42370607882) passes: 55 successful checks and four intended skips, plus successful Snyk. The old head's CI was superseded by this correction and is not counted as a pass. From `server/`: ```sh node ../cli/node_modules/tsx/dist/cli.mjs ../packages/db/src/test-postgres-command.ts -- node ../node_modules/vitest/vitest.mjs run src/services/native-runtime/native-harness-filesystem-independence.integration.test.ts src/services/native-runtime/native-harness-original-volume.test.ts src/services/native-runtime/native-harness-filesystem-independence-continuation.integration.test.ts --hookTimeout 90000 --maxWorkers 1 --fsModuleCache ``` ## Risks This changes a maintenance trust boundary. It proves web-byte preservation, not provider recovery or termination. External recovery obligations and existing resume failures remain. Unknown layouts, missing manifests, active local owners and changed authority fail closed. Invalid receipts are not automatically replaced. The inventory has independent limits of 128 entries, 16 MiB per file and 64 MiB total. Larger valid data stays on the original volume and blocks this mode. Canonical credential exclusions remain excluded. Evidence uses the existing encrypted ledger and retention roots; it does not become an executable backup. Old receipts remain byte-compatible. Startup adds bounded per-retained-scope database reads. Measure the affected cohort's actual serving startup cost before enrollment. Validation adds no filesystem or object read, worker or recurring poll. Live source qualification and publication remain separate after review, merge and normal delivery. ## Model Used OpenAI Codex, GPT-6 family, with reasoning, repository tools and PostgreSQL/filesystem test execution. The runtime does not expose a more specific serving model ID or context-window size. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-07 06:16:04 -06:00
DottaandPaperclip	585c885168	fix: preserve prepared sources held by provider artifact failures (#19810) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Online workspace migration archives local files before it changes their storage authority. > - A failed provider session can leave an active board-owned recovery hold over a prepared local source. > - The existing migration owner accepts finalized sources and workspace-export failures. > - It rejects a settled provider-artifact failure even when the prepared source and recovery allocation have complete bindings. > - This PR permits that exact preservation case under the existing source and finalizer locks. > - The remote recovery hold remains active. The archive preserves local bytes and the existing recovery recipe. ## Linked Issues or Issue Description Refs #19642 and #19805 for the existing online migration and source-closure owners. **What happened?** Online workspace migration rejects a prepared source held by a terminal `runner_remote_provider_artifact_incompatible` recovery. This also blocks another local workspace that shares the Git source. The provider session had executed work. A pre-execution exemption would be unsafe. **Expected behavior** Preserve the local source through the existing immutable archive owner when the board recovery, task version, terminal run, finalizer, and declared allocation all match. Keep the remote recovery action and authority unchanged. **Steps to reproduce** 1. Create a prepared native source and a failed run with provider session and tool events. 2. Set its finalizer to an unowned terminal artifact failure. Add the matching active board recovery and task status version. 3. Remove the local descriptor and inspect or migrate a shared local Git alias. 4. Before this change, the source proof is rejected. The regression fixture reproduces this failure. **Paperclip version or commit** Reproduced on master `1674902b4f`. The final branch is based on `5a92d53f7d`. ## What Changed - Accept only the matching active board-owned artifact failure with a current task block, no live execution authority, an exact producer fingerprint, and a declared prepared-source allocation. - Include the task version and complete existing source/recovery evidence in publication revalidation. - Lock the proven recovery tasks in sorted company scope before publication checks. A held descendant task produces the existing busy error. - Add a real PostgreSQL regression with 124 tool executions, a missing descriptor, shared Git aliases, immutable download, and cold restore of the local archive. - Add stale, foreign, owned, controlled, malformed, and publication-race rejection cases. - Document that this archive preserves local bytes and the recovery recipe. It does not prove remote export or release the remote hold. ## Verification - Genuine baseline RED: the positive migration regression rejects the source before the production fix. - Focused treatment: 12/12 PostgreSQL cases pass. - Review-race RED: both a selected source and a Git companion published while a descendant recovery task was locked. The corrected tests reject both cases. - Two affected owner suites after the lock repair: 91/91 pass in 23.18 seconds. - Strict server TypeScript check passes after the lock repair. - Module boundaries and `git diff --check` pass. - [Current-head CI](https://github.com/paperclipai/paperclip/actions/runs/42367152081) passes: 56 successful checks, four conditional skips, and one neutral review check. No checks remain pending or failed. - Greptile and Paperclip reviews are both 5/5 on `0a6e6c3ece`, with no open findings. - The first descendant fixture attempt hit the immutable task/privacy guard before it reached the race. The corrected fixture creates that task binding at admission and produces the two genuine REDs described above. ## Risks - A broad classification could let a migration move local authority without a complete recovery recipe. The new branch requires the exact failure, producer, task version, source allocation, and released execution owners. - Evidence can change during upload. Existing locks and full publication revalidation reject those races. - The remote allocation may contain changes absent from the local source. This PR preserves only local bytes and the durable recovery route. It does not mark remote work exported, finalized, or safe to discard. - No schema, provider lifecycle, admission, or polling behavior changes. ## Model Used OpenAI `gpt-6.1-sol`, with reasoning, tool use, and local code execution. The context window size is not exposed. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-07 05:27:55 -06:00
DottaandPaperclip	d2efe3392b	fix(native): preserve retired authority evidence (#19806) ... ## Thinking Path > - Paperclip manages work that AI agents perform for users. > - Native sessions retain control-plane files when execution authority moves to a later run. > - Volume migration must preserve these historical bytes before a server can stop depending on its old volume. > - The existing preservation owner archives the current controller and supervisor, but refuses a nonempty authority-epoch directory. > - A settled four-run session can therefore remain blocked after its current controller archive is complete. > - This pull request adds a closed historical inventory to the existing encrypted evidence archive. > - The benefit is preserved source evidence and database-only replacement validation without granting execution or recovery authority. ## Linked Issues or Issue Description Refs #19748. A search of pull requests for filesystem independence and issues for authority-epoch history found no duplicate change. This fixes its uncovered historical-file case. **What happened?** A settled native session retained three prior controller files in authority-epoch directories. Its three historical database checkpoint headers were absent. Maintenance preserved the current controller, then refused filesystem independence because those historical files remained uncovered. **Expected behavior** Preserve the exact historical bytes and modes through the existing encrypted evidence owner. Keep original files, prior archive rows, run outcomes, warnings, stamps, session pointers, and recovery policy unchanged. Validate the resulting receipt on a replacement without the source volume. **Steps to reproduce** Use the included four-run fixture with a current-controller-only archive, three prior authority epochs, destroyed provider receipts, released ownership, and absent historical checkpoint headers. Call the canonical filesystem-independence owner. The base rejects the nonempty directory; the treatment preserves the complete evidence and validates it after removing source-volume identity from the test process. **Paperclip version/commit** Baseline `ef83d566cacf1d5f740d701560597dad2bfa4619`; final branch rebased onto `27170dca49`. **Deployment mode** Original-volume maintenance followed by an ephemeral replacement. This PR performs no hosted migration or provider operation. ## What Changed - Add optional closed authority-epoch entries to the existing `original_volume_source_evidence` archive. Preserve nested file bytes and modes through the existing encryption, readback, ledger, audit, and retention owners. - Bind each epoch to its retained run, canonical checkpoint identity when present, or explicit header absence plus the exact admitted authority binding. Keep current-source checkpoint and artifact checks strict. Historical evidence never becomes an executable checkpoint. - Recheck the complete historical inventory at archive and receipt publication fences. Keep physical locks, all-run ownership and termination checks, source capability checks, and final CAS. - Bind the history inventory and its database facts into the authenticated archive manifest. Replacement validation uses database bindings only. Later header presence, removal, retirement, or changed identity invalidates the receipt. - Leave history-free manifest bytes and receipt shapes unchanged. Keep an existing current-controller-only archive when a later complete archive is added. Unknown children and other nonempty history directories remain blockers. ## Verification - Node 24.22.2, PostgreSQL 18.1, macOS arm64. The final four-run fixture fails on the baseline owner at its nonempty-history guard. The same final fixture and treatment pass all 51 focused PostgreSQL/filesystem cases. - The positive case performs actual encryption, object-store persistence, authenticated restoration, and exact byte/mode comparisons. It proves replacement database-only validation with absent source paths and storage reads refused. - Controls cover foreign identities, unknown children, owned prior runs, changed bytes or new files after upload, missing or newly present historical headers, malformed and retired headers, an unknown authority override, receipt-identity tampering, and a late concurrent winner. Existing current-controller evidence and history-free manifest bytes remain intact. - The baseline/treatment driver restored only its two owned source files in `finally` and verified their exact hashes. Earlier setup and treatment failures remain recorded: missing bundled PostgreSQL library links, an overly narrow raw-schema check, and an incorrect synthetic transient-workspace binding. The final baseline and treatment use the corrected same fixture; those earlier attempts are not counted as passes. - Review follow-up `21183b75f4` closes the missing-history-field gap. Deleting history from an actual published receipt reproduced an invalid true result before the fix. Unconditional manifest reconstruction now rejects it; all 46 owner cases pass. Genuine history-free manifests retain their exact bytes. - Review follow-up `f3d305dd36` adds suspended historical Runner-state bytes and mode checks through authenticated restore, active/foreign state refusals, exact 16 MiB and 64 MiB boundaries, and retention of an oversized file without publication. All 51 cases and server TypeScript pass; production behavior is unchanged. - CI run `42362784772` on the previous head had one unrelated 30-second timeout in `manual-private-cell-report-assets.test.ts`, with 6,864 support tests passing. The failure remains recorded. The prior head `21183b75f4b223cd3ec28124cdc194f24b4f79ba` passes [required CI run 42363408227](https://github.com/paperclipai/paperclip/actions/runs/42363408227), including Runner support: 55 successful checks and four intended skips, plus successful Snyk. The final test/documentation head `f3d305dd3690a7db38b57c4a77389c17206cb76b` passes [required CI run 42364958386](https://github.com/paperclipai/paperclip/actions/runs/42364958386): 55 successful checks, four intended skips, one neutral review check, and successful Snyk. Fresh Greptile is 5/5; all four review threads are resolved. No timeout or assertion was weakened. - The count warning is resolved as independent bounds: the actual descriptor accepts 32 control-plane-only epochs (97 entries) and 32 epochs with 31 Runner states (128 entries), and rejects 129 entries. The 32-epoch and 128-entry maxima both apply; the capture budget is unchanged. - Server TypeScript and module-boundary checks pass. The local verification planner selects ten broad application lanes; required CI supplies that wider coverage instead of duplicating it locally. - Reproduce the focused owner suite from `server`: ```sh node ../cli/node_modules/tsx/dist/cli.mjs ../packages/db/src/test-postgres-command.ts -- node ../node_modules/vitest/vitest.mjs run src/services/native-runtime/native-harness-filesystem-independence.integration.test.ts --hookTimeout 90000 --maxWorkers 1 --fsModuleCache ``` ## Risks This changes a maintenance trust boundary. A source capture is limited to 128 entries, 16 MiB per file, and 64 MiB total. These limits are intentionally below the Runner's 256 MiB state maximum. Larger valid epochs remain on the original volume and continue blocking filesystem independence. It uses bounded directory reads and file descriptors, rejects aliases and unknown paths, and rechecks bytes before publication. Storage failures retain original files and ledger evidence; they do not settle recovery or authorize a retry. Startup adds bounded database reads for retained historical header bindings or their absence. It adds no source filesystem or storage reads. The selected cohort's serving startup cost still needs measurement before enrollment. Other historical layouts require their own canonical source qualification. No missing provider history is declared recovered, and no automatic corruption repair is added. ## Model Used OpenAI Codex, GPT-6 family, with reasoning, source editing, shell tools, and PostgreSQL/filesystem test execution. The runtime does not expose a more specific serving model ID or context-window size. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-07 04:55:18 -06:00
DottaandPaperclip	f673bd3cb5	fix(native): verify legacy harness filesystem independence (#19748) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Native sessions retain provider checkpoints and recovery state across turns. > - Server replacement must preserve every remaining local data dependency. > - A legacy backup stamp can outlive a destroyed provider and an absent local backup. > - Surviving skill files can already have exact immutable package copies. > - Raw controller files also contain stream events that database checkpoints omit. > - This pull request records verified filesystem independence under the original-volume maintenance owner. > - Replacement startup checks durable bindings while existing resume failures and policies remain intact. ## Linked Issues or Issue Description Refs #19715, #19729, #19733. **What happened?** Startup treats every retained legacy backup stamp without a current backup row as a local filesystem dependency. This also blocks sessions whose provider was already destroyed and whose remaining local skill bytes have exact durable copies. **Expected behavior** An authorized maintenance owner can prove that an exact retained source has no uncovered local harness payload. Startup can use that proof after replacement. The proof must preserve failed recovery state and must not invent a provider backup. **Steps to reproduce** 1. Retain a terminal native session, its checkpoint, and its legacy backup stamp. 2. Record exact canonical destroyed-provider receipts. Keep only admitted immutable skill files on the original host. 3. Publish the owner-verified independence receipt. The old startup predicate still blocks; the updated predicate validates its durable bindings. ## What Changed - Add an internal original-volume capability. It requires a private nonce anchor, independently reviewed attachment evidence, current reserved runtime identity, and a witness that is at most 120 seconds old. - Verify retained and selected-source inputs, checkpoints, leases, destroyed-provider receipts, released ownership, and exact immutable skill references. - Inspect canonical persistence roots and compare surviving skill bytes and modes. Refuse any provider directory present outside the current persistence profile, including an old Codex home after a preconfigured-home switch. Unknown data, backups, history, owners, or source changes still block publication. - Preserve raw controller and supervisor bytes through the existing encrypted evidence archive owner. Match recovery records to the database checkpoint, authenticate the exact archive row, and compare the original bytes again before publication. The archive grants no executable authority. - Publish one audited receipt with source locks and a final comparison. Keep original files, stamps, warnings, statuses, and session pointers. A late capture retains a valid published winner and refuses an invalid receipt. - Validate published receipts from current database bindings on replacement hosts. Add no startup filesystem probe, object read, provider call, or recurring worker. ## Verification - Genuine baseline regression: restore the original startup predicate while keeping the actual receipt owner. The positive PostgreSQL/filesystem case fails with expected `false`, actual `true` after valid publication. Restore the changed predicate; the case passes. - Final rebased head `e78f4b4424`: 42 affected PostgreSQL/filesystem cases pass. This includes 32 owner guards, three paired continuation cases, six existing failed-source archive controls, and one existing lease-verified backup migration control. The other 113 tests in the selected existing files were explicitly unselected. - Genuine controller baseline: the unchanged prior owner publishes no raw archive and accepts missing checkpoint parts. Both new regressions fail. The repair passes encrypted byte-for-byte controller/supervisor restore, missing checkpoint, foreign source, active source, and changed-after-upload controls. - Genuine omitted-provider baseline: the unchanged owner accepts old Codex, OpenCode, and ACPX history after a preconfigured-home switch. All three refusal cases fail. The fix passes those cases and permits preconfigured execution with no omitted directory. - Genuine late-publication baseline: both concurrent winner tests fail before the repair. The repair keeps the existing valid receipt, refuses an invalid one, and keeps one audit event. A delayed raw upload also retains the first authenticated archive and its receipt. - Capability controls: 12 passed, including empty replacement refusal, stale or future evidence, changed deployment, missing volume, path aliases, changed anchor, and current remount identity. - The actual server-to-Runner boundary preserves explicit recovery policy on original and empty homes. The separate actual CREATED-sandbox preparation callback preserves checkpoint identity and policy without a backup. Provider I/O and final transport construction are controlled. - Warm sessions retain the same canonical refusal on both homes, make no backend/provider attempt, and retain the saved checkpoints. - Server TypeScript, module boundary checks, diff checks, and a private-data scan pass. The Runner TypeScript build was refreshed after rebase to include two new upstream exports. - Fresh Greptile review is 5/5 with no unresolved threads on `e78f4b44240b0fc33c2fd7cae2d5b4a2578e3153`; check `128330103712` completed successfully. Required CI remains pending. No live preservation or enrollment action ran. Focused command from `server/`: ```sh node ../cli/node_modules/tsx/dist/cli.mjs ../packages/db/src/test-postgres-command.ts -- node ../node_modules/vitest/vitest.mjs run src/services/native-runtime/native-harness-filesystem-independence.integration.test.ts src/services/native-runtime/native-harness-filesystem-independence-continuation.integration.test.ts src/services/native-runtime/native-controller-migration.integration.test.ts src/services/native-runtime/native-harness-backup-storage.integration.test.ts --testNamePattern 'owner-verified|legacy harness continuation|preserves a failed source online|migrates a lease-verified' --hookTimeout 90000 --maxWorkers 1 --fsModuleCache ``` ## Risks - This proves that no uncovered harness payload remains local. It does not recover provider history or certify that no other copy exists. Existing governed-wait and warm-session failures remain. - Unknown providers, retained owners, extra payloads, missing references, or changed source bindings fail closed. Invalid receipts require investigation; this change does not repair or replace them automatically. - The maintenance capability requires independently reviewed Railway attachment evidence. The original anchor remains stable across normal releases; each new staging invocation needs current deployment and mount evidence. - Startup validation adds bounded per-scope database reads. It pages candidate scopes and caps each source history at 500 rows. Measure the affected cohort's actual startup latency on the qualified serving build before enrollment. - Raw archives use the existing backup ledger, encryption, retention, and restore machinery. They preserve evidence only. They do not repair missing provider history or grant a new resume policy. - Local tests control provider and transport boundaries. Live staging remains a separate step after review, merge, normal delivery, and a fresh original-volume capability. ## Model Used OpenAI GPT-6 through Codex, with reasoning, repository tools, and local code/test execution. The exact runtime variant and context-window limit are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-07 00:57:20 -06:00
DottaandClaude Opus 5.5	7e3caa7bac	fix(tree-control): resume work a pause gate refused after release (#19421) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - The board can pause an issue tree. A pause stops work. Resume or release must continue that work once. > - PR #19394 made release re-dispatch a run that a pause Stop cancelled. > - That rule covers only a run that an operator Stop ended and that the hold snapshot named. > - A scheduled retry that comes due during a pause is not stopped. The dispatch gate cancels it with `issue_paused`. The release did not see it as owed work, so the task stalled with no run. > - This pull request makes every gate that refuses work for a pause record the covering hold. Release then re-dispatches that work exactly once. > - The benefit is that a paused task with a parked retry or a queued run continues after release, with no manual wake. ## Linked Issues or Issue Description Refs #19394 **What happened?** A child task had a `workspace_busy` scheduled retry. The board paused the parent tree. The retry came due during the pause. The scheduled-retry gate cancelled it with `issue_paused` ("Scheduled retry suppressed because the issue is held by an active subtree pause hold"). The board released the hold. Four minutes later the child was still `in_progress` with no run, no execution blocker, and no new activity. **Expected behavior** Release (or `mode: "resume"`) re-dispatches the refused work exactly once. No reconciliation and no user message are necessary. Stranded-issue recovery does not add a second run. **Steps to reproduce** 1. Give an assigned child task a parked `workspace_busy` scheduled retry. 2. Pause the parent tree. 3. Let the retry come due while the pause is active. The gate cancels it with `issue_paused`. 4. Release the pause. No run starts for the child. **Paperclip version or commit** master at 4d49a31286 (includes #19394). **Agent adapter(s) involved** Not adapter-specific (core bug). ## What Changed - `issue-tree-control.ts`: add `ISSUE_PAUSED_ERROR_CODE` and `pauseSuppressionResult()`. A gate records `treeHoldSuppression: { holdId, rootIssueId }` on a run that it refused for a pause. - `findOwedPauseResume` now treats the latest run as owed when it is an `issue_paused` cancellation under a pause hold. It uses the recorded hold. For an unmarked run (a scheduled retry cancelled before this change), it uses a snapshot pause that was active at cancellation. The operator Stop rule does not change. - Scheduled-retry gate (`run-dispatch/adapters/postgres.ts`, `cancelSuppressedRetryInTx`): locks the pause row `FOR SHARE` and records the covering hold. A concurrent release either sees the refusal, or the retry sees no pause and runs normally. - Queued-run claim gate (`heartbeat/queue.ts`): cancels with `issue_paused` and the hold marker, after the agent start lock is released. Before, the cancel re-entered that lock from inside it, and the agent's queue stalled until the 30-second stale-lock timeout. After the refusal is saved, the gate re-checks the hold and resumes the task itself if release already finished (`resumeIfPauseAlreadyReleased`). - Release (`issue-tree-resume.ts`, route): revisits the snapshot members and every task with a run refused for that hold, also when `wakeAgents` is set. This covers tasks created under the tree after the snapshot and tasks moved out before release. - `packages/db`: partial index `heartbeat_runs_tree_hold_suppression_idx` (migration 0436, `CREATE INDEX CONCURRENTLY`, registered as a top-level migration) for that lookup. - Docs: `doc/execution-semantics.md` (gate-refused work, race handling, non-assignee and pre-fix scope) and `doc/DATABASE.md` (index). ## Verification - Red before the fix, green after: `pnpm --filter @paperclipai/server exec vitest run src/__tests__/issue-tree-pause-resume-run.test.ts` (21 tests). - "resumes a parked retry the pause suppressed exactly once after release / resume / legacy": before, `expected [] to have a length of 1` (no resumed run). After, one `issue_tree_resumed` run with `interruptedRunId` = the suppressed retry, no execution blocker, and the task finished. `reconcileStrandedAssignedIssues` added no run during the hold or after release. - "resumes a queued run the claim gate refused during the hold exactly once": before, the test timed out at 15 s (start-lock re-entry). After, the run is cancelled with `issue_paused` and the hold marker, and release re-dispatches it once. - "resumes a refused retry on a task moved out of the paused tree before release" and "... on a task outside the snapshot when release also wakes members": review findings, one resume each. - "leaves a due retry parked when the pause is released while the gate refuses it": the test waits until the gate blocks on an uncommitted release. The retry is not cancelled and runs once. Without the `FOR SHARE` lock the gate does not wait and the test fails. - "resumes work a gate refused after the release that should have resumed it had finished": the late-refusal re-check resumes once, and a repeated check does not dispatch again. - "does not resume a paused-code cancellation that no pause hold covered": negative case. - Related suites pass locally: `src/__tests__/issue-tree*`, `src/modules/run-dispatch`, `src/services/heartbeat/queue.test.ts`, `heartbeat-dependency-scheduling`, `heartbeat-workspace-busy`, and `packages/db` `client.test.ts`. - I did not run a live staging check here. Staging APIs are not reachable from this environment. ## Risks - Migration 0436 adds a partial index on `heartbeat_runs`. It is built concurrently and covers only cancelled runs with the marker, so it is small. - The scheduled-retry gate now takes a `FOR SHARE` row lock on the pause hold before it cancels. Release updates that row, so the two serialize briefly. Release does not lock issues or runs, so the lock order cannot deadlock with the gate's issue-then-run locks. - The queued-run claim gate now records `issue_paused` in place of the generic `cancelled`. Stranded recovery already classifies `issue_paused` as non-retryable. The pause resume owns that work, so recovery does not add a second run. - Scope limits (documented): a non-assignee run refused by a pause is not replayed, the same as non-assignee wakes that admission drops during a hold. Among pre-fix rows, only scheduled retries carry `issue_paused`, so only those fall back to the snapshot. A pre-fix row whose hold is already released does not self-recover; the staging task that showed this bug needs one manual wake, or a new pause and release. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - Claude Opus 5.5 (Anthropic), model ID `claude-opus-5-5`, used through Claude Code with tool use (shell, file edits, test execution). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-06 03:03:15 -06:00
3 people	f2593b7905	feat: make Coordinator and Agent Chat standard and speed up navigation (#19360) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - People enter that work through the workspace, agent conversations, and tasks. > - Coordinator and Agent Chat still require experimental enrollment. > - Task link prefetches do not warm the compact queries used by the default task view. Chat also waits for a request when its navigation list already holds the conversation. > - This pull request makes Coordinator and Agent Chat standard and reuses the reads needed for navigation. > - People can choose Classic workspace in Experimental settings. Cached work can appear while fresh data loads. ## Linked Issues or Issue Description **What existing behavior does this improve?** Workspace selection, Agent Chat availability, and navigation between Chat, Tasks, and task details. **Subsystem affected** Cross-cutting: UI, workspace preferences, instance settings, and the database migration. **Current behavior** People must enable Coordinator and Agent Chat in Experimental settings. Opening a task can repeat requests because prefetch warms the full detail and comment queries, while the default view reads compact task data and a recent comment window. Opening Chat waits for a detail request even when the current person's conversation list contains it. **Proposed behavior** Coordinator is the standard workspace for everyone. Experimental settings offer Classic workspace, off by default. Old Coordinator experiment values do not select Classic. Agent Chat is available to everyone, including instances with an old saved or managed off value. Task link intent warms the queries used by the mounted view. Chat can use the current person's company-scoped conversation list during refresh. **Reason and benefit** People can use the standard workspace without setup. Repeat navigation can show cached content while the server refreshes it. **Breaking changes** Existing Coordinator experiment and Agent Chat off values no longer disable these surfaces. Classic requires an explicit new opt-in. The workspace API keeps its existing response shape and audit checks. The migration retains legacy values and adds a separate Classic preference. Execution permissions, company access, and chat privacy checks still apply. **Additional context** Roadmap check: this graduates existing surfaces and improves their navigation. It does not add a new agent execution capability. Duplicate searches found no open Coordinator workspace PR. Related server cache work, Refs: #17828, addresses compact issue-list invalidation; this PR addresses client navigation queries. ## What Changed - Add a default-off Classic workspace preference. Derive the existing workspace API response from that choice. Keep personal persistence, account isolation, and audited writes in the workspace preference service. - Replace the Coordinator experiment control with Classic workspace. Use Coordinator while preferences load. Update the existing settings examples and navigation recipe. - Retire the Agent Chat experiment control. Ignore old stored and managed off values. Retain the compatibility key and the existing execution and access checks. - Reuse account- and company-scoped chat list data with its original freshness timestamp. - Share compact task and recent-comment query options between prefetch and the task view. Keep full-history prefetch for Classic tasks and expanded history. - Add upgrade, replay, cache, account isolation, and browser switching regressions. Update product, database, development, and roadmap documentation. ## Verification - Targeted preference, settings, migration, cache, and UI regression tests passed during implementation. The cache tests hold refresh requests pending and check that content still renders. They also check account isolation and stale refresh behavior. - A real browser test verified fresh Coordinator defaults, Classic opt-in persistence, and return to Coordinator. It used an isolated source checkout with fresh data on macOS. - Token, migration numbering and safety, map, and Storybook catalog checks pass after the rebase. - Repository typecheck and build pass. Typecheck and token gates also pass after review repairs. The broad local run passed all six chat integration shards (1,931 tests). It then found the host-CLI-dependent recovery fixture described below. Its remaining duplicate work was stopped after the full current-head CI matrix passed; this is not a claim that the broad local command completed green. - Review repairs passed 419 UI/migration fixture tests, 19 Coordinator navigation tests, and all 214 tests in the five affected server suites. The 24 Chat/workspace browser tests pass, including standard Coordinator switching and explicit Classic persistence. - The broader browser repair run passed 85 tests. It retained two failed assertions and skipped five later serial cases. The affected files then passed all 11 tests after the fixes: reopen the desktop panel after reload and open More for Audit and Connectors. This includes the five serial cases that had not run. - The broad local suite exposed a recovery fixture that executed the host Codex CLI during a simulated remote probe. On a host with Codex 0.154.0, model fallback broke its fixed-model assertion. The fake sandbox now reports Codex 0.160.0. All 20 selected recovery/provider compatibility cases pass after the repair. - A CLI company import/export suite timed out during server startup in the second CI run. The port fallback is intentional in that fixture. No root cause was established. That suite passes on the final commit in CI. This records recovery, not a claimed product fix for the earlier timeout. - The first CI run exposed remaining assumptions about the retired flags and Classic UI. The repair commit updates those fixtures and navigation steps. It also restores the missing enabled Cases destination in Coordinator. Earlier local recovery attempts used the wrong fixture notification and advanced fake time during live execution; the corrected tests use the subscribed recovery queue and wall time during execution. - Greptile reviewed commit `98972b030d4505d838427a2fca6b196b8cad6d47` at **5/5** with no new comments. The original finding is resolved. - Current-head CI is green: **56 successful checks**, with three checks skipped by workflow filters. This includes typecheck, build, the complete Vitest matrix, all eight browser shards, Runner verification, release checks, and security checks. [Final CI run](https://github.com/paperclipai/paperclip/actions/runs/42132651414). - Typecheck caught missing `pid` and `startedAt` fields in the simulated command result. The fixture now returns the complete process contract, and the server test-layer typecheck passes. - Storybook catalog alignment was checked. Storybook play tests were not run. Hosted latency and cold bundle loading were not measured. ## Risks - The new default changes the workspace for people who previously left the Coordinator experiment off. They can opt into Classic in Experimental settings. - The additive migration must run before the new server code. It is safe to replay and preserves explicit Classic choices. - Cached content can be stale during background refresh. Existing query invalidation and source timestamps still control freshness. - These changes reduce avoidable loading waits. They do not establish a measured improvement in hosted request latency or initial bundle download time. ## Model Used OpenAI Codex, based on GPT-6, with reasoning, repository tools, code execution, and browser automation. The exact serving revision and context-window size are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Scott Tong <scott@scottsmbpm5max.lan> Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-05 16:28:25 -08:00
DottaandClaude Opus 5.5	bf10bc695a	feat(task): show the agent's context window in task properties (#19273) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Agents run through a harness (Codex app-server, or Claude through ACPX), and the runner turns harness events into Paperclip events > - Both harnesses report how full the model's context window is. Codex sends `modelContextWindow` with its token usage. Claude sends `used` and `size` in ACP `usage_update` > - Paperclip dropped both values. The task view could not show how close an agent is to compaction, and a compaction left no visible mark in the task chat > - This pull request carries the context-window occupancy through the runner, stores it with the existing usage events, and shows it as a "Context" row in the task Properties panel > - It also shows a "Context compacted · 230k → 38k tokens" divider in the task chat when the agent compacts its context > - The benefit is that operators can see when a long task is near its context limit and when the agent lost detail to a compaction ## Linked Issues or Issue Description Refs #19252 (same pattern: a canonical harness event turned into task-chat UI). Refs #19267 (status notices; it turns Claude's compaction banner into a notice, and this PR reads that notice too). **What existing behavior does this improve?** The task view shows no context-window information, and a compaction is invisible in the task chat. **Subsystem affected** Runner usage normalization (Rust and TypeScript transport), the PRP usage schema, a read-only issue API, the task Properties panel and the task-chat transcript. **Current behavior** Codex `modelContextWindow` and ACP `used`/`size` are dropped in the runner. `context.compacted` always has null sizes, Claude compactions emit no `context.compacted` event at all, and the live runner turn hides every marker except "interrupted". **Proposed behavior** `usage.reported` carries an optional `context {usedTokens, windowTokens}`. The task Properties panel shows a Context row ("10% of 258k") with a hover breakdown (tokens used, input and cached input, output, cost, compactions). The transcript shows a compaction divider, with sizes from the usage before and after the compaction. **Reason and benefit** Operators can see when a long task is close to its context limit, and they can see where the agent's earlier context was summarized. **Breaking changes** None. The new schema field is optional, and the new endpoint is read-only. ## What Changed - PRP `usage.schema.json`: add an optional `context {usedTokens, windowTokens}` object. Regenerate the schema bundle and the protocol manifest. - Rust `provider_events.rs`: add `codex_context_usage` (last request `totalTokens` and `modelContextWindow`) and `acpx_context_usage` (ACP `used`/`size`). ACPX `usage_update` now sets `context`. - Rust `provider_backend.rs`: Codex `thread/tokenUsage/updated` sets `context` on live (non-historical) usage. - Rust `provider_events.rs`: emit `context.compacted` for the completed `context_compaction` provider notice that #19267 produces from Claude's compaction banner. Only this path marks a Claude compaction, so the server counts each compaction once. - `runnerd-codex-transport.ts`: `rehydrateRunnerdUsageNotification` keeps a valid `context` on `tokenUsage`, so it reaches the stored `item.completed` usage item. - Server: new `GET /api/issues/:id/context-usage` (issue read access is required) and `issueContextUsage` service. It reads only the assignee's current session (the session of its newest usage report), and returns that session's latest context reading, non-zero totals, cost, and the count of compactions across all of the session's runs. Added to OpenAPI. Shared type `IssueContextUsage`. - DB: migration 0432 adds two partial indexes on `heartbeat_run_events`, built concurrently. One indexes usage items by run and time. The other indexes `context.compacted` events by company and session. `EXPLAIN` shows that both lookups use them. - UI: new `ContextUsageMeter` (bar, percentage, hover card) and `IssueContextUsageRow` in the Execution section of Properties. The row refreshes every 8 s while a run is active, and once more when the run ends. - UI transcript: `native-run-events.ts` maps `context.compacted` to a `context` activity entry with pre/post sizes from neighbouring usage items. `transcript-adapter.ts` turns it into a new `context_compacted` marker variant. The live runner turn keeps that marker as its own timeline row. - Storybook: `task-context-window.stories.tsx` (Properties panel in a task, all states, hover breakdowns, divider). ## Verification - `cargo test -p paperclip-runner-core --lib provider_events` (new tests: ACPX context, Codex context, banner compaction, notice compaction) - `pnpm --filter @paperclipai/paperclip-runner exec vitest run src/live/runnerd-codex-transport.test.ts` - `cd ui && npx vitest run src/components/ContextUsageMeter.test.tsx src/components/transcript src/components/task-chat src/components/issue-properties` - `cd server && npx vitest run src/__tests__/issue-context-usage.test.ts` (embedded Postgres) - `node scripts/typecheck-low-memory.mjs`, `pnpm check:token-gates`, `pnpm --filter @paperclipai/paperclip-runner run check:protocol-types` - Live check on a local worktree instance through the runnerd path: - A Codex `gpt-5.5` task showed "10% of 258k" (27k of 258k, input 77k with 49k cached, output 1.1k). - A Claude Sonnet 4.6 task showed "17% of 200k" (34k of 200k). - Storybook: Tasks and conversations / … / Task chat / Context window. - Not verified live: a real compaction. The divider is covered by unit tests through the same projector path the task chat uses. ## Risks - The schema field is optional, and older runners omit it. The UI renders nothing until a harness reports a window. - Migration 0432 builds two partial indexes concurrently on `heartbeat_run_events`, which is a large table. The indexes cover only usage items and compaction events, so they stay small. They add a little write overhead to those events. - Claude in-progress usage rows still record zero tokens with `requests: 1`. The final turn usage is correct. This PR does not change accounting. - A "Compact now" action is out of scope. It needs a compaction-only run that does not produce a run result. It will come in a follow-up. ## Model Used - Claude Opus 5.5 (`claude-opus-5-5`), Anthropic, used through Claude Code with tool use (shell, file edits, in-app browser for Storybook and the live instance). ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-05 16:54:27 -06:00
DottaandPaperclip	dbbde744d2	fix(workspaces): preserve finalized recovery holds through offline import (#19180) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Offline workspace import must save files before local volume removal. > - A task recovery hold can remain after native file finalization succeeds. > - The old importer rejects that hold even when its file source is exact and no controller owns the run. > - Clearing the hold would discard the task's recovery obligation. > - This pull request saves files and carries each exact recovery source forward without resolving the hold. > - Accepted-result finalizers keep their existing retry path. ## Linked Issues or Issue Description Refs #19144, #18943, #19038. This PR builds on merged #19144. **What happened?** Offline import reports `workspace_recovery_unresolved` for terminal native runs with finalized workspace references and active task recovery holds. Some holds also name an exact historical file allocation. **Expected behavior** Save the workspace durably. Keep task warnings, recovery rows, results, coordinator phases and task pointers unchanged. Retain exact future file recovery and accepted-result finalization retries. **Steps to reproduce** 1. Retain a local task workspace and an active recovery hold for a finalized native run. 2. Stop all application writers through offline maintenance. 3. Attempt workspace import. 4. Observe that the old importer rejects the hold. ## What Changed - Add an owner module that checks the exact terminal native run, finalized reference, released ownership and task relationship. - Require the normal finalizer's successful company/run/task receipt for an accepted-result retry. Support historical receipts without a workspace foreign key. - Validate recorded file allocations with the existing recovery-source owner. - Journal and recheck hold evidence. Lock recovery, coordinator, run and allocation rows before publication. - Give finalized file sources a separate migration marker. Keep legacy execution-replay suppression out of accepted-result retry paths. - Use the owning parser for older finalized references that omit optional fields. - Redirect future file recovery to immutable snapshot preservation. Keep provider-stop and source checks intact. - Verify native copyback or snapshot receipts for each exact allocation. Require proof for every source, including completed mixed repairs. - Retain existing successful copyback receipts. Keep a historical folder's obligation on its real source workspace. - Retain the finalized migration marker through the execution blocker projection. Discover finalized child-task sources from their exact ancestor workspace reference. - Document the receipt and lock contracts. ## Verification - Fresh local run at head 6ebe535751: 208 tests pass across the new preservation suite, migration suite, publication concurrency suite and legacy restore recovery suite. - `node ../node_modules/vitest/vitest.mjs run --config vitest.config.ts src/services/finalized-workspace-recovery-migration.test.ts src/services/remote-workspace-migration-concurrency.test.ts src/services/remote-workspace-migration.test.ts src/__tests__/legacy-workspace-restore-recovery.test.ts` from `server/`. - Comment-only cleanup `a858d203c68a6c86fd39e30fb63dc56c1a303429` removes added prose comments under CONTRIBUTING.md. TypeScript 6.0.3 output with `removeComments: true` is byte-identical before and after for all six changed TypeScript files. Runtime behavior and the 208-test evidence are unchanged; no new tests were added for this cleanup. - The two file-restoration cases fail against the original importer with `workspace_recovery_unresolved`. - Positive tests delete the old folder and restore the saved archive. They compare unchanged task, recovery, result and coordinator rows. - Negative controls cover unknown kinds, mismatched sources, malformed file markers, active ownership, active recovery and changed evidence during upload. - Red/green tests exercise getExecutionBlocker and the ancestor import path. An accepted result without a successful finalize receipt remains blocked. - The mixed-receipt regression fails before the review fix and passes afterward. A missing secondary receipt still blocks repair. - Existing and future repair receipts remain readable. Accepted-result finalization still returns its original successful receipt. - Local server typechecking passed before the master replay. The post-replay local check found a stale linked Runner declaration in unchanged vendor code. Clean current-head CI Typecheck + Release Registry and Build both pass. - Greptile gives current head `a858d203c68a6c86fd39e30fb63dc56c1a303429` 5/5. All actionable findings are fixed and resolved. - The prior CI run had one workspace shard cancelled after its spot runner received a shutdown signal. No test assertion failed in that job. That incomplete run was superseded by the equivalent comment-only cleanup. The fresh full CI run passed on the current head; the original infrastructure cancellation remains recorded here. - [Current-head full CI](https://github.com/paperclipai/paperclip/actions/runs/41970385102) passes: 54 success, one neutral and two skipped statuses, with no failed or pending checks. Typecheck, tests and build pass. - Ponytail's source review rates the behavior head 5/5. It did not execute tests; the local and CI runs above supply execution evidence. - No provider, serving migration or copied-data deployment acceptance is claimed. ## Risks - This path depends on the existing offline deployment fence. It does not prove that providers stopped. - Unknown or unverified source boundaries remain blocked. - Migration receipts must remain exact. Missing or changed finalized file-source receipts fail closed. - Root maintainers own merge, deployment and copied-data acceptance #19144 is already merged. ## Model Used OpenAI GPT-6.1 Codex, exact model ID `gpt-6.1-sol`. Used for reasoning, code editing, shell tools and test execution. The runtime does not expose its context-window size. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-04 23:15:11 -06:00
DottaandPaperclip	0eaabe5c0b	refactor(accounting): remove company serialization from paid settlement (#18917) ... Settle paid operations through operation-scoped transactions. Preserve exact ledger evidence and replay while moving aggregate budget decisions to durable deferred work. Co-Authored-By: Paperclip <noreply@paperclip.ing>	2026-11-04 07:29:28 -06:00
DottaandPaperclip	de9f263454	fix(workspaces): prevent preservation lock cycles (#18918) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Remote workspaces save files before a later task turn can use them. > - Admission, preparation and preservation share task, run and workspace rows. > - Snapshot inserts also lock their foreign-key parents. > - Different acquisition orders could form a PostgreSQL deadlock and delay saved-file recovery. > - This pull request orders those runtime parents and refuses busy legacy publication owners. > - Files and ownership evidence remain available without replaying provider work. ## Linked Issues or Issue Description **What happened?** Snapshot reservation and publication could hold a workspace while waiting for a task or run. Other workspace owners could hold that parent while waiting for the workspace. Review also found reverse preparation, provisioning and legacy-import paths. Real PostgreSQL owner-pair tests reproduce `40P01`. **Expected behavior** Concurrent owners must complete or retain their normal ownership refusal. A lock cycle must not interrupt file preservation. **Steps to reproduce** 1. Prepare a remote workspace with retained files in disposable PostgreSQL. 2. Schedule actual save and reserve, preserve, prepare or provision functions on opposing rows. 3. Release the scheduling barrier. 4. Unfixed source deadlocks. Fixed source saves the files or returns its normal ownership hold. The tests also schedule an actual legacy import beside an arriving reservation and a stale native status commit. **Paperclip version or commit** The original three save regressions fail on unchanged master `ce7766dc11c4515190d48d395f26a90bba900f8a`. Reverse preparation, provisioning and imported no-op controls fail on published `2d13b3f`. The additional import-publication and native-status owner pairs also have causal PostgreSQL RED/GREEN proof. **Deployment mode** Source checkout with PostgreSQL and real filesystem commands. Snapshot encryption and reload use local object storage. No hosted storage, live model or original-task recovery claim. Related: Refs #18908, whose preservation acceptance exposed this separate fault. This repair has no code dependency on that PR. Refs #17846 for separate legacy terminalization locks. Refs #18746 for the documented admission order. Repository search found no existing repair for this owner graph. ## What Changed - Lock company, current task and run before the runtime workspace. Recheck the run binding and pin save-operation attribution. - Apply that order to reserve, prepare, provision and both save transactions. New shared-workspace provisioning receipts use the current task. - Lock import source parents before reservation and publication. Recheck the source binding and retain the publication fingerprint. - Use full-strength `NOWAIT` locks for legacy coordinator, run and allocation rows. Only PostgreSQL `55P03` becomes `remote_workspace_migration_blocked:execution_rows_busy`. The publication transaction rolls back. Other errors propagate. - Preserve writer, epoch, snapshot, foreign-key, Stop and owner checks. Keep command, capture and upload I/O outside row-lock transactions. - Add actual-owner concurrency, unknown-effect, eventual retry and rollback controls. Document each owning transaction and its foreign-key edges. ## Verification - Node 24.22.2 and pnpm 9.15.4: all 107 save-concurrency, migration-concurrency and migration tests pass. - All 81 enabled disposable-PostgreSQL integration and lifecycle controls pass on the final head. Both opt-in database variables point to a dedicated local test database; no skipped case is counted as qualification. - Actual preparation/provision/import no-op peers reproduce three deadlocks on the prior source. The fixed owners preserve and reload files. The real provisioning command runs once; a lost response remains an unknown effect and is never replayed. - Actual legacy publication versus reserve and stale native status commit also reproduce deadlocks before repair. Busy run/lease controls preserve the journal, archive and files, then finish from the same journal after release. - A real publication constraint failure rolls back earlier coordinator, profile and snapshot writes. Its original database error propagates. - Immutable same-company and foreign-task guards, writer/epoch loss and uploaded-object retention pass. Four real shared/inherited reuse cases fail old receipt attribution and pass current-task attribution. - The original spontaneous issue-foreign-key failure did not retain its peer statement. These controlled owner pairs prove supported defects; they do not identify that historical peer. - Commands: `pnpm exec vitest run server/src/services/remote-workspace-save-concurrency.test.ts server/src/services/remote-workspace-migration-concurrency.test.ts server/src/services/remote-workspace-migration.test.ts`. Enable the separate lifecycle suites only with their documented disposable test database variables. - Full recursive typecheck and `pnpm build` pass on production commit `dacf6278abd3257c407a297c6db8872e76d85f61`, using Node 24.22.2 and pnpm 9.15.4. Current head `4c1d7769e6cfa9536a67c4e3b536cef155f19966` changes only the canonical PostgreSQL host-support guards. All 18 changed concurrency cases executed and passed with zero skips; their server test-layer typecheck passes. All 57 current-head check contexts are terminal and clean: 53 passed, two skipped and two neutral. Required `ci / verify` and `ci / e2e` pass. Greptile and Paperclip both reviewed exact current head at 5/5 with no actionable findings. There are no open review threads. - Composition with #18908 includes this exact parent history. Its production-composed head passed 724 affected tests, all 81 enabled integration/lifecycle controls, recursive typecheck and build on Node 24. Its final test-only guard head passed the 18 changed concurrency cases and their test-layer typecheck. This is local server/PostgreSQL/native-backend-boundary evidence, not a hosted model or storage claim. - The required broad local Vitest attempt stopped at an unchanged chat publication-batch test with `socket hang up`. The earlier CI workspace shard timed out in the unchanged CLI chunked-ZIP test. Both failures remain recorded; neither is reported as a pass or hidden by timeout changes. The chat case passes one bounded focused head/base control, so the original full-suite socket failure was not reproduced by that control. ## Risks - Short transactions take parent-row locks earlier. Competing writers can wait for those transactions. - Administrative import now refuses a busy native owner. It retains its journal and archive for a later explicit retry. - Native owners have different lock orders. The import's nonblocking requests avoid a new global native lock policy. - Missing bindings and uncertain command effects remain holds. The repair does not infer termination, release an executor or replay external work. - No schema, foreign-key or timeout change. ## Model Used OpenAI Codex, GPT-6 family. The exact serving model build and context window are not exposed in this agent session. The agent used reasoning, terminal tools, code edits, PostgreSQL and filesystem tests. A separate Codex agent reviewed the production ownership graph. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-04 07:17:40 -06:00
DottaandPaperclip	612d9931a6	Support per-turn Runner sessions on ephemeral web servers (#18932) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - The web server controls native Runner sessions in remote sandboxes. > - An ephemeral web server must recover without its previous local filesystem. > - The existing admission rule accepts warm sessions. Managed Claude, Grok, and OpenCode sessions resolve to per-turn execution. > - Per-turn execution also needs durable provider-session bytes after the sandbox is retired. > - This pull request adds encrypted backup publication and removes the warm-only admission rule. > - Both lifecycle modes can use the existing native ownership and checkpoint contracts during a web deployment. ## Linked Issues or Issue Description Refs: #18518, #18529, #18826, #18835, #18841, #18864, #18887. **What existing behavior does this improve?** Native Runner execution on web servers with `PAPERCLIP_EPHEMERAL_SERVER=true`. **Current behavior** The admission rule requires a warm Runner lifecycle. Managed provider credentials can resolve an agent to per-turn execution, so enabling the ephemeral deployment profile blocks those turns. A database controller checkpoint does not preserve provider files after the old web home and per-turn sandbox are removed. **Proposed behavior** Admit native execution in either resolved lifecycle. Keep provider and credential choices unchanged. Publish encrypted provider state to shared storage before sandbox cleanup. Restore it from a fresh web home for the next turn. Use the existing controller lease and generation checks for active takeover. **Reason and benefit** Operators can remove the web server volume without excluding per-turn providers or forcing managed accounts into warm sessions. New native Daytona profiles automatically enter both rolling-deployment qualification lanes. **Breaking changes** The additive migration creates a backup publication ledger. Existing volume-backed local-disk installations retain their local backup path. S3 installations publish encrypted backups and require a stable secrets master key. Existing-volume enrollment must import surviving session data before detaching the volume. ## What Changed - Admit native Runner execution independently of its warm or per-turn lifecycle. Keep host-owned legacy execution excluded from ephemeral deployments. - Store private provider state as encrypted objects. Journal uploads before I/O, read them back, and fence publication against the current native owner. Keep the previous published backup when storage or ownership checks fail. - Restore exact provider bytes into a private cache. Require an exact durable backup before sandbox cleanup. Extend the existing bounded retention pass to retire stored objects without adding idle polling. - Import selected legacy controller and provider state in the existing offline maintenance process. Preserve queued work, task pointers, pending recovery, and original files. Prefer canonical database checkpoints. - Preserve already-failed legacy controllers with missing original artifact proof as encrypted archives. These archives do not become execution authority. Successful retained sessions still require proof. Report archival and executable imports separately. - Verify unmanaged Grok API keys through the existing xAI account validator. The live test exposed a readiness gap that kept remote Grok agents paused after platform checks. Preserve failed credentials and the separate runtime warning. - Ingest Grok whole-prompt usage at the owning ACP boundary. Bind the receipt to the exact outbound request/session; reject replay, conflicts, and incomplete authority. Separate turn cost from cumulative session cost in the sidecar schema and Rust normalization. Preserve managed billing identity and identify direct xAI API credentials. - Preserve published workspace directory names across cold allocations, including destroyed-allocation cleanup. Keep unpublished epoch/lease directories isolated and refuse to overwrite an occupied preparation. This fixes the cold-session identity regression exposed by #18922. - Increase bounded checkpoint-header inspection to 1 MiB. Retain the aggregate inspection limit. - Register all nine native Daytona profiles in per-turn and warm rolling-deployment suites. Delete the entire departing server home, exercise ordinary reads and writes, require active ownership transfer, then check a later turn on another fresh server. Permit only exact notification replay after reconnect. Ownership stays with the existing modules: Runner validates its protocol state; Core validates run scope and controller ownership; storage owns object I/O; the maintenance process owns offline conversion; the E2E wrapper owns process replacement and probes. No provider protocol is added to the shared admission rule. Grok receipt parsing stays in its provider module. The shared sidecar gains an explicit cost basis because its existing price field means session-cumulative spend, while Grok reports prompt totals. Existing consumers retain cumulative behavior when the new field is absent. ## Verification - Focused native admission, archive validation, publication fencing, cleanup, readiness, legacy import, and E2E observer tests pass. Real PostgreSQL cases verify that queued intent and historical recovery rows stay unchanged. - Full typecheck and build pass on the rebased branch. The review follow-up passes server typecheck, 29 focused PostgreSQL/archive/readiness tests, and module-boundary checks. Revision fb8d39a7a1 reached 55 successful CI checks and Greptile 5/5 with no unresolved threads. The Grok follow-up passes Runner/server typechecks, 238 ACP runtime/projection/usage tests, 16 sidecar-schema tests, the Rust cost regression, and Core billing regression. The e9aae9cf revision passed all 57 successful checks, with 5 skips and 2 neutral checks, and exact-head Greptile 5/5. The latest 9cbec30a4f follow-up changes only E2E catalog/admission controls; its 291 affected tests pass, all 57 check contexts succeeded (5 skips, 2 neutral), and exact-head Greptile is 5/5 with no open review threads. - Migration numbering and safety checks pass. - A local real PostgreSQL/S3 roundtrip preserved 2,870,101,591 payload bytes across 89,100 archive entries after deleting the source directory. Restored SHA-256 matched; upload/readback took 56.5 seconds, restore 74.8 seconds, process peak RSS was 1.40 GB, and all fixture resources were removed. - Archives preserve contained relative links, reject link chains/traversal, and enforce independent byte/entry/object limits. Offline verification streams hashes. Orphaned deleted-run backups stay on the original volume. Obsolete object retention preserves the selected backup, live lease references, and pending uploads with owners. - Isolated API-key Codex deployment: original active runner/session transferred to the replacement and committed. All 567 reads, 57 writes, and 57 readbacks succeeded. A second replacement completed a same-session continuation with all 287 reads and 29 writes succeeding. The strict cell failed two agent-authored shell commands; this result is retained as failed. - Isolated API-key Claude deployment: original active runner/session transferred and committed. All 584 reads, 59 writes, and 59 readbacks succeeded. A second replacement completed a same-provider-session continuation, with 211 reads and 22 writes succeeding. The strict cell failed an initial completion call that omitted a registered attachment citation; the agent corrected it. This result is retained as failed. - Isolated API-key OpenCode deployment: the same active runner/session transferred and committed. All 481 reads, 49 writes, and 49 readbacks succeeded. A second replacement retained the provider session and completed useful work, with 156 reads and 16 writes succeeding. The strict cell failed agent tool calls: a denied external-directory write, malformed artifact hashes, and a second completion after the first result was committed. There was one submitted/completed turn and one committed result; reconnect notification replay was identical. This result is retained as failed. - Grok's real first turn now completes with settled usage and provider cost ($0.41397); the next turn is admitted normally. That attempt then exposed a shared workspace-path identity regression before deployment. Three cold-restore cases reproduced it before the fix; 106 workspace/transport tests and four focused cold-restore cases pass afterward, including destroyed allocation and occupied-directory preservation. Server typecheck and build pass. At b5b0dbb03f both controller switches passed the read/write probe without failure, and the active runner retained its process while the controller generation advanced. The third turn exposed an invalid reasoning-token subset check; ad07e681ba fixes it with the actual receipt regression. Two later live attempts failed with an upstream Grok rate limit before deployment. A tiny preflight prompt succeeded before the second attempt, but the full workload was still rate-limited. The final live gate remains incomplete. No accounting or identity guard was bypassed. Earlier failed attempts and their exact resource-cleanup receipts remain recorded. - Earlier Codex/Claude/OpenCode receipts predate #18922; they establish their tested revisions. Current-head live qualification remains pending; #18943 separately preserves pre-enrollment logical/provider workspace addresses and adds actual legacy migration proof. Its first Codex migration attempt stopped safely at skill-version verification. - Earlier attempts remain recorded: missing local provider-pack setup blocked one Claude launch, and the observer rejected identical reconnect replay in another. Setup and the observer were corrected before the latest run. - Named staging enrollment has not started. Its serving revision and post-deployment journeys remain separate delivery gates. - Broader E2E harness validation exposed deployment-catalog and installed-lane coverage drift; the affected 291 controls now pass. Twelve other failures reproduce on unchanged base 1a39dea9aa. They concern cleanup call expectations, dated operating-overhead fixtures, a Pi profile-version expectation and workflow-security expectations. No baseline failure is reported as passing. ## Risks - Provider archives can contain credentials. Objects use authenticated encryption with scoped associated data and a wrapped data key. The original stable master key remains required. - Storage failure prevents publication and sandbox cleanup. Operators must keep shared storage available and preserve the previous volume during enrollment. - Legacy state without verified identity cannot become executable recovery authority. Archival preserves evidence and existing failures; it does not recover already-lost provider files or clear blocked tasks. - Local overlap probes establish the tested application behavior. They do not establish Railway routing behavior or live managed-subscription qualification. ## Model Used OpenAI Codex, based on GPT-6, with reasoning, tool use, code execution, and live integration tests. The exact runtime variant and context-window size are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [ ] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-04 02:12:51 -06:00
4 people	ce332ecec0	fix(execution-admission): keep admitted project sets after settlement (#18871) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - #18746 added execution-admission storage: one admission row per attempt and one charge row per admitted project. > - Settlement deletes every charge row. The admission row keeps only the primary project and an opaque context revision. > - Thus, after settlement, the complete admitted project set is lost. > - A retained provider session still carries the references of its previous admission. Example: a task mentions A and B, the admission settles, and then a user removes B from the task text. The next admission must still count B, or start a fresh context. The primary project or the context token cannot supply B. > - This pull request keeps the complete admitted set on the admission row after settlement. Charge rows stay the only active capacity. > - The benefit is that later retained-session resolution can read the previous set. Settled history does not hold capacity or block project deletion. ## Linked Issues or Issue Description Refs #18746 (corrects its storage). Related: #2831, #14333. **Subsystem affected** Server execution admission (`server/src/modules/execution-admission/`) and the `packages/db` schema. **Problem or motivation** `settleAdmission` deletes all charges of an admission. No other storage records the complete project set. After settlement, the set cannot be recovered. Current task text is not a replacement, because it can change after admission. **Proposed solution** Add `execution_admissions.admitted_project_ids uuid[]`. It holds the sorted, distinct set. It is written once at admission and a trigger blocks changes. It has no project foreign key. `{}` is a known empty set. Null means unknown. Only settled rows can have null. Migration `0428` fills the set of unsettled `0426` rows from their charges, because those charges are still complete. Settled `0426` rows stay unknown. **Alternatives considered** - Keep charge rows after settlement with a `released_at` column and a partial active index. The project foreign key would then block project deletion permanently, or the key must be removed from active charges. One table would also hold two different facts. - A separate history table with one row per project. This is more rows, joins and constraints for data that is only read as a whole set by admission ID. - Encode the set in `context_revision`. That token is opaque and owned by the context owner. The database cannot validate it. - Use `heartbeat_runs.context_snapshot`. It is mutable and is per run, not per admission attempt. ## What Changed - Schema and migration `0428_retained_admitted_project_sets`: add `admitted_project_ids`, a check (null only when settled, no null elements, at most 100 entries) and an immutability trigger. The backfill fills unsettled rows from their charges and leaves settled rows null. The migration is safe to run again. Migration `0426` is not changed. - `recordAdmission` writes the set. A replay compares against the stored set. `settleAdmission` still deletes the whole charge set in one transaction and does not change the stored set. - Add `readAdmittedProjects` (company-scoped, by admission ID). It returns `known` with the set, or `unknown`. - Add a pure `retainedSessionProjects` rule: a retained session uses previous ∪ current. An unknown previous set returns `fresh_context_required`. No consumer uses it yet; C1b integrates retained sessions. - Update `doc/DATABASE.md` and `server/src/modules/README.md`. Not changed: no public cap writes, no claim or dispatch integration, no session integration, no provider activation, no `serialize` → cap 1 migration. Active counts still use only the indexed charge rows. ## Verification Red, on unchanged `master` code, with the new tests: - `server`: `npx vitest run src/modules/execution-admission/adapters/postgres.test.ts`. The new tests fail. With a temporary reader that uses the only storage `master` has (charges), the settled A+B admission reads `[]` instead of `[A, B]`. - `packages/db`: `npx vitest run src/execution-admission-migration.test.ts` fails, because no `0428` migration exists. Green, with this change: - `server`: `npx vitest run src/modules/execution-admission`: 27 passed. The new PostgreSQL test covers: A+B admission → settlement → set still readable, charges and counts zero, settlement replay keeps the set, a second attempt with a different set, primaryless and empty sets, company isolation, rollback, immutability, the check constraint, and deletion of a project that has only settled history (its ID stays in the set). It also checks that a project with an active charge still cannot be deleted. - `packages/db`: `npx vitest run src/execution-admission-migration.test.ts`: 2 passed. The upgrade test starts from the shipped `0426` schema with an unsettled A+B row, an unsettled empty row and a settled row. After the upgrade the sets are `[A, B]`, `{}` and null. A second run of `0428` changes nothing. - `pnpm --filter @paperclipai/db typecheck` and `check:migrations` passed. `node scripts/check-module-boundaries.mjs` passed. - Not run locally: the server layered typecheck. The local process was killed for memory (a 5.8 GiB limit shared with other jobs). CI runs it. This PR does not prove C2 claim races or C3 lifecycle authority. ## Risks - Migration: one `ADD COLUMN`, an `UPDATE` that only touches unsettled rows (none in production, because nothing writes admissions yet), a check and a trigger. It does not delete or rewrite data. - Settled rows created before `0428` stay unknown. A future consumer must start a fresh context for them. It must not treat them as empty or primary-only. - The stored set has no project foreign key. Company scope is checked at admission time, under the same project locks and the charge foreign keys. Size: about 70 production lines (schema 8, migration SQL 22, adapter 28, domain 15), 105 test lines and 24 doc lines. Generated metadata (`0428_snapshot.json`, `_journal.json`, removal of `0422_snapshot.json` by the standard pruning) is separate. ## Model Used - Anthropic Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use (shell, file edits, embedded PostgreSQL tests). Default context window and reasoning mode. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) Co-authored-by: nickyleach <331803+nickyleach@users.noreply.github.com> Co-authored-by: Paperclip <noreply@paperclip.ing> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>	2026-11-03 15:31:10 -08:00
4 people	fef86e32e9	feat(execution-admission): add project concurrency policy and admission storage (#18746) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Projects group tasks. Agents run tasks as heartbeat runs. > - Today, workspace mode and shared-workspace flags decide whether tasks run at the same time. A project cannot set its own limit on concurrent task executions. > - A correct project limit must count every project that a task uses, including @-mentioned projects. It must also keep the count when a project is archived or deleted, and when a run is admitted more than one time. > - This change cannot go into one pull request with claims and settlement. Thus this pull request adds only the policy semantics and the durable accounting storage that later claims will use. > - This pull request adds a new `execution-admission` module, three tables and the deletion guards. No route writes a cap and no claim path enforces it. > - The benefit is a tested storage contract (constraints, idempotency, rollback, indexed counts, lifecycle preservation) before any behavior changes. ## Linked Issues or Issue Description Refs #2831, Refs #14333 (related agent-level and adapter-level limits; not duplicates). **Subsystem affected** Server execution admission (new module `server/src/modules/execution-admission/`) and the `packages/db` schema. **Problem or motivation** A project cannot limit how many of its task executions are active. The current shared-workspace flags mix resource safety with capacity. A future project limit needs storage that records each admission attempt and every project that the attempt charges. Run IDs cannot be the identity, because a run can be released before dispatch and admitted again. **Proposed solution** Add a separate policy table that keeps "never configured" apart from "explicit no limit". Add admission epochs with one charge row per distinct project. Settlement deletes the charge set in one transaction. Later pull requests integrate claims, settlement, waits and the public control. **Alternatives considered** Columns on `projects` would leak an unenforced cap through every project reader. A project column or a `uuid[]` on `heartbeat_runs` cannot enforce per-project uniqueness or company scope. `budget_reservations` has no project set. A counter would be a second source of truth. ## What Changed - Added `project_task_execution_policies`. No row means never configured. A null maximum means an explicit "no limit". A check accepts only positive maximums. A composite foreign key keeps the project and company together. The row is deleted with its project. - Added `execution_admissions`. Each row is one admission attempt of a run: `(run_id, attempt)` is unique, and a partial unique index allows one unsettled attempt per run. It keeps the context revision, the nullable primary project (provenance, no foreign key) and the settlement identity. A check sets `settlement_id` and `settled_at` together. - Added `execution_admission_project_charges`. It has one row per distinct admitted project, unlimited projects included. Composite foreign keys keep the admission and the project in one company. The project foreign key has no cascade, so a charge cannot disappear with its project. `(company_id, project_id)` is indexed for active counts. - Added migration `0426_absent_guardian.sql` (renumbered from `0423`, then `0425`, as master added `0423`–`0425`). The generated SQL was reordered so the unique indexes exist before the composite foreign keys that need them. Snapshots `0419` and `0420` were pruned to keep five snapshots. - Added the `execution-admission` module (domain → application → adapters): - Domain: policy patch parsing and application (omitted keeps, null clears, partial updates keep other fields, malformed values are rejected), canonical project-set preparation (primary ∪ references, deduplicated, ascending, bounded with an explicit `too_many_projects` result), and the settlement replay decision. - Application: internal `readTaskExecutionPolicy` and `updateTaskExecutionPolicy` commands. No route, tool, CLI or import calls them. - Adapter: the project-set lock (`FOR NO KEY UPDATE`, ascending, one statement), the policy store, and the storage transitions `recordAdmission`, `settleAdmission` and `countActiveProjectCharges`. These transitions are not exported from the module entry point. Claims (later) must add the capacity check and the lifecycle evidence. - Project deletion returns `409 project_execution_admission_pending` while the project has a charge. Agent deletion returns `409 agent_execution_admission_pending` while its runs have an unsettled admission, and removes settled history. Company deletion calls a new module participant before it deletes runs and projects. - Documented the tables, the lifecycle rules and the proposed global lock order in `doc/DATABASE.md`. Added module ownership to `server/src/modules/README.md`. ## Verification - `cd server && npx vitest run src/modules/execution-admission` → 2 files, 26 tests pass (the Greptile finding on an empty primary ID added an assertion to an existing test). The adapter tests use embedded PostgreSQL and cover: - policy semantics, the maximum check and the company foreign key; - charges for every distinct project, a primaryless set and an empty set (no rows); - replay of one admission ID, conflict on a changed record, refusal of a second live attempt and the partial unique index; - settlement of the whole set once, replay, a different settlement, then attempt 2 for the same run; - company isolation of projects, runs and admission IDs, the duplicate-charge key, and rollback of an aborted transaction; - active counts per project, and an `EXPLAIN` that uses `execution_admission_project_charges_project_idx`; - archive keeps charges, `projectService.remove` returns 409, a direct project delete fails on the foreign key, and delete succeeds after settlement; - `deleteAgentDependencies` returns 409 while unsettled, and `deleteCompany` removes only that company's admissions. - `cd packages/db && npx vitest run src/execution-admission-migration.test.ts` → pass. It removes the new tables and receipt, seeds a legacy project and run, applies pending migrations, and compares the existing rows. - `pnpm --filter @paperclipai/db check:migrations` → pass. Five snapshots remain (`0421`, `0422`, `0424`, `0425`, `0426`; `0423` is SQL-only on master). - `node scripts/check-module-boundaries.mjs` → pass. - `packages/db` `tsc --noEmit` → pass. A scoped `tsc` of the module entry points and domain tests → pass. - Existing tests for the changed deletion services → 6 files, 161 tests pass (`resource-lifecycle-events`, `prompt-injection-prevention`, `agent-lifecycle/lifecycle`, `case-deletion`, `project-workspace-root-provenance`, `companies-service`). - Not run locally: the full `server` typecheck. `tsc` and `tsgo` were stopped by the out-of-memory killer on the 7 GB machine (exit 137, also single-threaded). The full `pnpm -r typecheck`, `pnpm test:run` and `pnpm build` were not run locally; CI ran them on head `520b69d553`: all gates pass, including Typecheck, Build and the 12 server test shards. After merging master (`1c9ca5829f`) into head `c088729361`, the migration check, migration upgrade test, module tests, module-boundary check and `packages/db` typecheck were rerun locally and pass; CI is rerunning the full suite. ## Risks - Migration risk is low. It creates three empty tables and indexes. It does not change existing tables or rows. - Behavior changes only when admission rows exist. Nothing writes them yet, so project, agent and company deletion behave as before. - Later claim work must take the project-set lock in the documented order. A claim that takes project locks after issue locks could deadlock with project deletion. - Settlement deletes charge rows, so a settled admission keeps its primary project and context revision but not its full project set. > For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and discuss it in `#dev` before opening the PR. Feature PRs that overlap with planned core work may need to be redirected — check the roadmap first. See `CONTRIBUTING.md`. ## Model Used - Anthropic Claude Opus 5.5 (`claude-opus-5-5`) in Claude Code, with tool use (shell, file edits, embedded PostgreSQL tests). Default context window and reasoning mode. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge 🤖 Generated with [Claude Code](https://claude.com/claude-code) --------- Co-authored-by: nickyleach <331803+nickyleach@users.noreply.github.com> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-03 11:35:28 -08:00
DottaandPaperclip	f7ad1dc7ca	fix(workspaces): make attached project repositories writable (#18770) ... ## Thinking Path > - Paperclip lets people assign work to AI agents and inspect the result. > - A task can use repositories from more than one project. > - Remote workspace preparation treated every additional project as a read-only source. > - This rejected valid Git repositories before the provider started, even when no source was read-only. > - The task page then hid the preparation reason behind a generic failed-attempt notice. > - This pull request prepares authorized repositories as writable task copies and shows redacted workspace validation errors. > - People can work across both projects and see the reason if folder preparation fails. ## Linked Issues or Issue Description **What happened?** A remote task with a selected Git-backed project and another mentioned Git-backed project failed before provider execution. It reported `remote_workspace_readonly_sources_unsupported`. Neither project had a read-only setting. The task notice showed only that the attempt failed. **Expected behavior** Each attached repository should be writable inside the task workspace. This should preserve source access checks and saved work. A workspace validation failure should explain its cause on the task page. **Steps to reproduce** 1. Configure remote workspace storage and a native sandbox environment. 2. Select a Git-backed project for a task. 3. Mention another authorized Git-backed project in the task. 4. Start the task. Preparation rejects the additional source before it starts the provider. **Paperclip version or commit** Reproduced against `dc9f387edc`, before this change. **Deployment mode** Managed remote workspace storage. Local regression checks use disposable PostgreSQL and independent filesystem processes. Related merged work: Refs #18403 and #18504. Those changes established remote storage and metadata-only references. They still reject configured cross-project repositories. No duplicate writable-repository repair was found. Refs #18774 for the test-only retention-fixture repair reused to unblock CI. ## What Changed - Add every configured Git repository of an authorized referenced project to `.paperclip-repositories/` as an editable task copy. - Retain saved paths, refs, pins and files. Recheck retained project access and source trust. Keep explicit read-only, local-source import and remote feature gates. - Keep committed snapshot repository coverage separate from later requests. Honor configured default refs, resolve remote branch names, and publish secondary checkouts only after checkout succeeds. Share configured-ref resolution between root and attached-repository scripts. - Include redacted workspace validation messages in the task interruption projection and existing failure notice. Preserve Retry permissions and render messages as plain text. Explain retained-folder access and trust denials while preserving the dedicated low-trust project-access path. - Add source, authorization, redaction, UI and save/restore regressions. Update the implementation contract and workspace maps. - Reuse the reviewed test-only repair from #18774. Batch the shared-workspace history fixture, verify its complete privacy-source map, and drain owned test bodies before cleanup. Production retention behavior is unchanged. ## Verification - Red before repair: four source-resolution cases failed with the reported read-only error. The task-error projection test also failed because it omitted the cause. - Green: 49 source and transport tests, 16 task projection and redaction tests, and 10 UI tests. The assembled preparation check passes. All 48 remote workspace lifecycle tests pass. The full preparation suite passed all 126 assertions but its cleanup hook exceeded 30 seconds. The unchanged base reproduces the same cleanup timeout with all 126 assertions passing. The focused preparation check finishes cleanly. - The real PostgreSQL/Git lifecycle checks cover both first-turn and later project attachments. They verify the configured release branch, saved edits, replacement allocations, unchanged source folders, committed archive contents, and released writers. - Review regressions were red before repair: the default ref became null, later attachment failed during restore, non-default remote branch checkout failed, and invalid secondary refs left partial checkouts. They now pass. - The local browser shows the workspace validation explanation and Retry action. The fixture uses a saved failed run; this proves the error display, not a successful live sandbox run. - `pnpm -r typecheck` and `pnpm build` pass. Map, module-boundary and token checks pass. - A local two-turn acceptance probe repeated at `17ed67eaa7` used real Codex CLI 0.165.0, `gpt-6-astra`, and `xhigh` effort. Codex wrote files in both task repositories. The services saved them, removed the first allocation and its Git sources, restored another allocation, and Codex read the saved files and wrote a follow-up in both folders. This uses the real source resolver and persistence services with a local command-runner stand-in for sandbox transport. It does not qualify Daytona, managed subscription forwarding, or the original task. The first probe waited for stdin; closing the test harness pipe fixed that setup error before provider work. - `pnpm test:run` passed the first chat shard, then failed one chat response concurrency assertion in the second shard. That case passes in isolation on this head. The same isolated chat case passes on the unchanged base. Both corresponding unchanged-base chat shards also pass (351 and 324 tests). The cause of the earlier wider-suite chat failure is not established. The preparation cleanup timeout and chat failure remain part of this record. - CI at `17ed67eaa7`: all other verification jobs passed. Browser shard 6 initially reported a request callback from the preceding test after teardown; its single unchanged-code retry passed. Server shard 10 timed out the 2,100-row retention confirmation fixture at 15 seconds on both attempts. That exact case passes locally, but the repeated CI failure required a repair. Its setup repeatedly rebuilt a shared-workspace privacy map. The logs and failures remain part of this record. - Reused the test-only repair from #18774 without changing its source file. At `ab774e9418`, all 54 retention tests and all 25 ordinary production privacy tests pass locally (79 total). Full CI [41650626903](https://github.com/paperclipai/paperclip/actions/runs/41650626903) passed on that commit, and its exact-head Greptile review was 5/5. The fixture preserves its 2,100 rows, query-bound assertions, privacy-source map, and completed-history test deadlines. - The additional review identified retained-source access/trust denials that still bypassed the workspace explanation. Real-resolver regressions reproduced both plain-403 failures before the correction. Both now yield a safe workspace validation explanation, while the dedicated low-trust denial and saved workspace remain unchanged. The optional duplicate ref-resolution block is also consolidated. - Final review corrections: 65 source, transport and error-projection tests passed, followed by all 48 lifecycle cases against an owned disposable PostgreSQL database (113 total). The initial combined command skipped the explicitly gated lifecycle suite; the subsequent dedicated invocation enabled and passed all 48. Full workspace typecheck and build pass. The first standalone lifecycle launcher lacked the repository TypeScript loader; rerunning with that loader resolved its import setup error. At previous head `7be02ea09c4ac76df560e8b517050cdf398f33f0`, full CI [41654422329, attempt 2](https://github.com/paperclipai/paperclip/actions/runs/41654422329/attempts/2) passed, Greptile is 5/5 on that exact head, and all review threads are resolved. The first attempt timed out the unchanged voice-session report/history case at 15 seconds; 3,027 cases in its shard passed. That exact case passed locally, then its single unchanged-code shard retry passed. The wider-suite timeout cause remains unproven. The completed Paperclip advisory check is neutral; its earlier findings are corrected. No staging deployment or original-task recovery is claimed. - Master advanced while checks ran, producing conflicts in two adjacent test additions. Merged `27d35314be` into this branch as `d5c8d552939c86056abf8fe10833881b2ade41a4`, preserving both workspace-error tests and the audited Stop/receipt tests. Kept workspace maps to minimal corrections under the updated map rule. All 82 source, transport and interruption cases, all 48 real-database save/restore lifecycle cases, full typecheck, build, and map checks pass locally on the combined code. Current-head [CI 41660719214](https://github.com/paperclipai/paperclip/actions/runs/41660719214) and Greptile are pending; the earlier verified head has not been merged. ## Risks - Additional remote project repositories are now editable task copies. Shared source folders and upstream push permissions do not change. - Snapshot coverage uses existing workspace metadata. Older workspaces capture their previous inventory at reservation; successful save publication advances coverage and snapshot identity in one transaction. No SQL migration is needed. - A retained copy can contain files from a project that is no longer mentioned. Preparation rechecks that project's current access and trust policy before reuse. - Explicit read-only descriptors still fail. Source-less projects remain metadata-only. Local folders still require import. No migration or provider-pack update is needed. - Error display reads only workspace validation errors. The existing run-secret registry and username censor run before display truncation. A redaction failure omits the explanation. - The retained fixture repair pauses its row trigger only within the isolated seed transaction, rebuilds the exact source map, and restores the trigger before commit. A rollback regression and 25 ordinary privacy cases pass. Its paged-case test budget honors the existing bounded inner waits; production deadlines are unchanged. ## Model Used OpenAI Codex, GPT-6 family, with reasoning, tool use and code execution. The exact serving model ID and context-window size are not exposed by this session. The test-only fixture changes are reused from #18774, whose model record identifies OpenAI GPT-6.1 Sol. The optional live acceptance probe uses `gpt-6-astra` with `xhigh` effort through Codex CLI 0.165.0. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-03 15:33:44 +00:00
Dotta	5dee4993f1	fix(server): distinguish aborted HTTP responses in access logs (#18781) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Operators use HTTP logs to investigate task updates and database contention. > - Node starts each response with status 200 before it sends any headers. > - The custom HTTP formatter printed that status when the client disconnected before a response. > - This made an aborted request look like a successful task update. > - This pull request labels incomplete responses as aborted and preserves error severity. > - Operators can distinguish HTTP delivery from database commit evidence. ## Linked Issues or Issue Description - Refs: #18753. - Related: #14369 removes writes from legacy comment attribution reads. This change addresses a separate logging defect. The missing-write incident in #18753 remains unconfirmed. We reproduced a misleading `PATCH /issues/:id 200` log when the client received no HTTP response. We did not reproduce an HTTP 200 delivered before the mutation committed. ## What Changed - Label premature connection closure as `request aborted before response` or `request aborted during response` in both success and error log paths. - Log aborts as warnings, including on routes whose successful polling logs are normally silent. Keep explicit errors and 5xx responses at error severity. - Keep private webhook paths and query values out of aborted-request logs. - Add real HTTP disconnect coverage and real PostgreSQL task-update tests with synthetic data. - Document that HTTP completion logs do not establish database commit or rollback. ## Verification - Baseline: the new HTTP disconnect test failed because the log said `PATCH /api/issues/synthetic-task 200` at info level, while the client received no response. - `node node_modules/vitest/vitest.mjs run server/src/__tests__/http-log-aborted-response.test.ts server/src/__tests__/http-log-redaction.test.ts server/src/__tests__/issue-update-lock-contention-postgres.test.ts` passed: 81 tests in 3 files. - `pnpm -r typecheck` and `pnpm build` passed. The build used a second clean clone at the exact PR commit. - GitHub CI completed at `e3e96d836119df5fa1c7f22615484265de5aa700`: 52 checks passed and two Storybook checks were skipped. Greptile returned 5/5 with no findings. - Local `pnpm test:run` passed all six chat shards (1,834 tests). Its general server stage then reported four failures. We stopped the run after preserving these results and comparing the failing cases. The later workspace and serialized stages were not completed locally. The full local suite is not green. - The four observed failures were the two OAuth concurrency cases in `tool-access-service.test.ts`, the bounded workspace conflict case in `workspace-runtime.test.ts`, and the `enableNativeRunner`-disabled stop-control case in `muse-control.test.ts`. - Comparisons used the same sanitized environment on unchanged master `2b14ec03a48f17606db53fd7fc0edc53bc930409` and this PR. Both OAuth cases pass in isolation on both revisions. The full tool-access file passes all 498 tests on the PR; master has a different 15-second timeout, with 497 tests passing. The workspace case passes on the PR but fails port-reservation setup on master. The Muse case passes on both. These results do not explain or clear the original broad-suite OAuth and Muse failures. - Tested on macOS arm64, Node.js 26.4.0, pinned pnpm 9.15.4, and disposable embedded PostgreSQL. The API fixture uses a synthetic process-adapter agent. No model provider runs and no production database or real credentials participate. - The PostgreSQL fixture verifies an actual lock waiter with `pg_blocking_pids`. A blocked issue update does not return 200 before release. After release, status, monitor policy, inline comment, and audit receipt are persisted before the completed response. - Holding the company row with `FOR NO KEY UPDATE` does not block these fixture writes. They return 200 with persisted data while the compatible parent-row lock remains held. - An injected database trigger failure returns 500 and leaves the issue, comment, and mutation audit unchanged. Two influence-attempt receipts remain under the existing documented cap policy. - The combined lock/disconnect/failure test verifies no delivered response, an aborted log, and rollback after an injected database failure. The injected failure is not evidence of the reporter's production root cause. - Source inspection at release `v2026.1023.0` (`1b4c803816e82b0265c8422e1a804327a7ed8c54`) finds the same unconditional success formatter and awaited issue-update transaction. That release was not runtime-tested. ## Risks - Log consumers that parse the literal method/path/status message must handle the aborted-request message. - Client disconnects during streaming or SSE responses also use the aborted warning. Expected disconnects may therefore produce more warnings. - A disconnected request may still commit after the client leaves. This change reports transport completion and does not cancel or retry mutations. - This PR does not close #18753. The original missing-write cause and a received-200-without-commit scenario remain unconfirmed. - Local full-suite failures remain unresolved despite green CI. Keep this PR in draft until that verification gap is accepted or resolved. > This is a targeted bug fix. ROADMAP.md does not list overlapping feature work. ## Model Used - OpenAI GPT-6 through Codex, with reasoning, tool use, code execution, and parallel subagent investigation. - The exact runtime model ID and context window size were not exposed to the agent. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [ ] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge	2026-11-03 09:26:03 -06:00
DottaandPaperclip	dd02595390	fix(db): retain hosted census construction callers (#18725) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Operators use a bounded database census to find expensive read paths. > - The hosted server combines application code and capture wrappers in generated files. > - Generic HTTP owners suppressed caller capture. Generated paths also failed the caller allowlist. > - This PR retains trusted query construction locations without source maps. > - Operators can distinguish application query sites while exact owners, privacy limits and capture bounds stay intact. ## Linked Issues or Issue Description Refs #17522, #17564. **What happened?** A real map-free bundle with two application query sites produces one callerless census group. This affects unowned queries and queries under the generic `http.request` owner. **Expected behavior** The census should distinguish trusted query construction sites. It must keep unknown calls unknown and preserve specific semantic owners without stack capture. **Steps to reproduce** Run the committed bundle test and pinned comparison helper. The helper bundles the actual capture module and real Drizzle, with a fake postgres-js client. It does not assign a fake path to an isolated mock caller. **Paperclip version or commit** Control: `09162fe893b464dd2ccdafd14bd3ef1611202a86`. The branch is rebased onto `1e3ab690b072bbf6a1c1f1d0454ea49315b2074c`; neither intervening commit changes this owner. ## What Changed - Keep the exact generic HTTP owner and add bounded caller capture only during the active census window. - Exclude capture wrapper frames with a local V8 stack boundary. Keep one static generated construction anchor for trusted root builders. - Keep unscoped bundled driver and relational paths unknown. Their first frame can belong to the ORM. - Cover exact application lines, alternate parameters, prepared builders, transactions, nested savepoints, privacy and inactive windows in a real bundled scaffold. - Add a portable pinned comparison helper and retained measurements. Existing group, page, byte, expiry and output-rate caps remain in force. ## Verification - PASS: 54 focused unit, real-bundle, existing runtime bundler and real-PostgreSQL tests. - PASS: database TypeScript check. - PASS at final head `b270b92821`: full local `pnpm -r typecheck` and `pnpm build`. - The first local `pnpm test:run` was stopped after two chat partitions passed (668 cases), because source changed during the run. This is partial evidence only. The fresh final-head full local command passed all six chat partitions (1,829 cases). Its general phase reported one failure in the unchanged workspace port-conflict test. The exact case then passed alone (1 pass, 178 skipped), and the unchanged full file passed 179/179. The original failure did not reproduce; its cause is unknown. The general phase was stopped after its remaining serial queue was measured at roughly three hours. Cancellation did not print the original assertion diff. The full command is failed/incomplete, not passed. Remaining general files, workspace-project phases and 164 serialized files were not reached. Fresh final-head CI passes all partitions. - Final-head code CI passes. Greptile is 5/5 with its thread resolved. Paperclip Review is delayed by an external review workspace recovery failure; it has not completed on this head. - Five serial alternating rounds per mode, 1,000 queries per sample, 40 retained samples, Node v24.22.2. Generic and unowned attribution rises from 0/1,000 to 1,000/1,000 across two exact application anchors. Specific owners stay stack-free. - HTTP median wall cost is 10.528 → 15.169 µs/query; process CPU is 15.461 → 17.662 µs/query, with noisy overlapping ranges. This is census overhead, not a product speedup. - Review failure retained: the existing runtime bundler test first failed because the public parser accepted arbitrary generated frames. The fix restores default rejection and permits generated frames only from the trusted builder boundary. The unchanged existing test now passes. - Full ranges, raw samples, proof boundaries and reproduction commands: https://github.com/paperclipai/paperclip/blob/b270b92821ae47c456a1b61d78c1593c5348ede7/doc/performance/2026-11-03-db-capture-hosted-callers.md ## Risks - Active generic HTTP census now captures stacks. More groups can reach the existing 2,048-group cap sooner. - Anchors identify construction sites in one exact generated build. They do not identify later async consumers, TypeScript lines or CPU owners. - Unscoped driver calls can remain unknown. This is intentional. - The no-network local fixture excludes deployed Sentry/OTel stack formatting and traffic effects. It does not establish exact hosted overhead. - Wrappers remain installed after expiry. Disabled, future and expired windows do not capture stacks. No schema, authorization, provider, or query behavior changes. ## Model Used OpenAI GPT-6.1 Sol (`gpt-6.1-sol`) with reasoning, code execution and repository tools. The host does not expose the context-window size. Independent review used the same model family. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [ ] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [ ] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-03 06:04:42 -06:00
DottaandPaperclip	a92f616cd0	fix(db): attribute bounded captures to execution owners (#18634) ... ## Thinking Path > - Paperclip manages agent work through shared server and database services. > - High query volume can spend main-thread time on SQL construction and result decoding. > - The existing bounded response capture counts rows and bytes, but it cannot name the operation that executed a query. > - Bundled callers can be missing, and measuring every parsed JSON value adds work to the diagnostic. > - This pull request carries a semantic execution owner into each measured query and bounds response sizing. > - Operators can rank query volume by owner before choosing a performance fix. ## Linked Issues or Issue Description Refs #17504, #17522, #17537, #17564. **What existing behavior does this improve?** The opt-in `PAPERCLIP_DB_RESPONSE_CAPTURE_WINDOW` diagnostic. **Subsystem affected** Database diagnostics and existing server execution boundaries. **Current behavior** The capture groups by table, operation, and builder caller. It cannot distinguish execution owners that reuse a prepared query. Bundled deployments need source maps for caller locations. The capture visits every returned value and serializes parsed JSON again to estimate its size. **Proposed behavior** Version 2 captures use fixed semantic owners for HTTP requests, delivery queues, execution phases, and budget work. They count completed calls, returned rows, errors, and completion wall time. They sample successful results 1, 17, 33, and so on, with fixed cell and string/byte limits. Complex values remain explicitly unmeasured. Semantic ownership works without source maps. **Reason and benefit** A short census can identify which operations issue the most queries or return the most rows. It preserves each query's execution owner through pooled connections, concurrent operations, and prepared-query reuse. It reduces diagnostic work without claiming per-query CPU attribution. **Breaking changes** Opt-in capture output moves from `entry.v1`/`summary.v1` to `entry.v2`/`summary.v2`. Sampled primitive byte lower bounds replace all-result byte estimates. Consumers must use the new fields and must not extrapolate them into a total. There is no database migration or application API change. ## What Changed - Added `withDatabaseOperation(owner, action)` to the DB package. The server owns semantic labels. Queries retain execution ownership in their completion closure. - Added fixed owners at existing HTTP, delivery, budget, and execution timing boundaries. Delivery work replaces the context of the producer that woke it. - Added complete call/row/error counters and completion wall durations within the existing bounded window. Durations include waits and are not CPU measurements. - Sampled and bounded primitive-value sizing. Complex and oversized values remain unmeasured. Known owners skip repeated stack extraction. - Preserved the deadline, group limit, paced output, query outcomes, and existing coverage exclusions. Updated the operator documentation. - Added real PostgreSQL owner-isolation and prepared-query tests, server scope tests, and plain bundled-runtime proof. - Moved projection-test and benchmark full-response sizing into an explicit test helper. Existing payload-size thresholds remain unchanged; these synthetic checks do not use the production sampler. ## Verification - Final-commit DB capture suites: 43 tests passed in 13.86 seconds against the actual PostgreSQL driver, including concurrent owners, prepared reuse, transaction failure, a dedicated client, sampling, and a query crossing the deadline. DB typecheck passed. - Server attribution and existing delivery/execution/budget suites: 53 tests passed. Final concurrent HTTP GET/JSON POST scope refinement: 5 tests passed. - Runtime bundle suite: 8 existing tests passed. The new no-source-map owner test passed after its fixture was corrected to use a driver thenable. An ordinary native Promise can bypass an overridden `.then`; the real PostgreSQL tests separately cover driver integration. - Observer-only experiment: three alternating pairs per case on Node 24.22.2, macOS arm64, 3,000 calls per run after warm-up. For an already-materialized synthetic JSON result, median capture CPU fell from 82.37 to 1.87 microseconds/call. For a 100-row primitive result, it fell from 8.10 to 4.40 microseconds/call. Every result retained identity and all calls were counted. The new diagnostic intentionally measures less byte data; these are observer costs, not database latency or a hosted application speedup. Disabled-case timings were below one microsecond/call and too small for a performance conclusion. - Final lifecycle regression: 28 unit tests and DB typecheck passed. Closing the last capture disables and replaces owner storage; overlapping captures retain it. - Final-commit full recursive typecheck passed in 38.38 seconds and full build passed in 40.81 seconds. The build stamp matches `83ed4ba9cebd68d48929c46f15ab32d5c0b9687b`. Focused server attribution tests also passed 5/5 before the test-helper-only migration. Full test acceptance will use the repository's parallel CI gates; the unsharded local command takes hours. - Verification failures retained: initial sandbox runs could not open local IPC/PostgreSQL listeners; permitted reruns exercised the real services. One old test expected JSON serialization and was updated to assert explicit unmeasured complex values. The first bundle fixture used the wrong promise boundary, as described above. A retained-callback regression also demonstrated that disabling and reusing the same AsyncLocalStorage instance could resurrect an old owner; replacing the instance after the last capture closes fixes that case. - The first CI run found older projection tests consuming the previous full-response fields. Those consumers now use the full-response test helper, preserving their byte thresholds. The two complete affected route suites plus helper tests passed 115/115 in 73.08 seconds. A temporary full-row query negative control then failed the unchanged 2,048-byte limit at 5,000,812 bytes and was restored; five other service suites passed 34/34 and the affected chat cases passed 3/3. All three previously failing CI shards passed on the corrected head. A local skill-list benchmark smoke check completed 255 captured queries with no in-flight queries or overflow; this was integration verification under concurrent test load, not a timing benchmark. - Two final-head runner jobs lost communication with GitHub before reporting a test result. One targeted retry of those jobs and their dependent aggregate passed. All 53 final-head checks passed, with 3 intentional skips; previously passing suites were preserved. - Hosted capture remains pending until the reviewed revision is deployed and a bounded window is explicitly configured. Reproduce the focused checks with Node 24 and the repository pnpm version: ```sh pnpm exec vitest run packages/db/src/response-capture.test.ts packages/db/src/response-capture-postgres.test.ts pnpm --dir server exec vitest run --config vitest.config.ts src/__tests__/database-operation-attribution.test.ts scripts/bundle-runtime.test.mjs pnpm -r typecheck pnpm build ``` ## Risks - Owner context is active while a valid future capture window is armed, up to 30 minutes before accounting starts. No-window and expired calls take the direct path. Diagnostics still add bounded work while enabled. - A nearest nested owner is reported. Broad `http.request` and unattributed groups remain visible; this does not identify every service callsite or SQL shape. - The existing census excludes tagged/raw explicit-execute/streaming paths and internal protocol commands. Its counts are not PostgreSQL transaction totals. - Completion wall time includes queue/database/network/scheduling waits. Concurrent durations overlap. Sampled bytes exclude complex values, large strings, and values beyond the sizing limits. - Activation is startup-only. Operators must choose the window after artifact preparation, allow rollout/warm-up time, and remove the expired setting afterward. ## Model Used OpenAI Codex, GPT-6 family, with code execution, repository inspection, and parallel agents. The exact deployment model ID and context-window size are not exposed in this session. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-11-02 12:12:21 -06:00
DottaandPaperclip	5e4cc01073	feat(workspaces): keep remote files off the webserver disk (#18403) ... Keep native sandbox workspace files independent of the webserver disk. Use encrypted saved versions and Postgres ownership so a replacement server can recover files and continue work. Enable the path by default for new eligible workspaces when durable storage is configured. Preserve explicit opt-outs and existing host workspaces. Include safe snapshot repair, Files access, import, migration and retention. Bound saved-Files resources, preserve imported Git recovery, reject unfinished Git operations, publish immutable concurrent captures, and verify permanent object-version deletion. Validated 471 targeted local controls, build/typechecks, all 40 CI partitions, fresh Greptile 5/5 and security review. The PR records original failed attempts and scoped retries. Co-Authored-By: Paperclip <noreply@paperclip.ing>	2026-10-31 14:54:01 -05:00
DottaandPaperclip	8ff812cdde	feat(chat): deliver proactive task messages to agent chats (#18374) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Agent Chat gives each person a persistent conversation with each agent. > - Tasks and routines produce results outside that conversation. > - Those runs need a safe way to bring a requested result back to the person. > - The server must select the agent's own chat and check the source task's access rules. > - This pull request adds proactive chat messages and unread indicators. > - People can see the result, open its source task, and reply in the same chat. ## Linked Issues or Issue Description **Subsystem affected** Server, native runner tools, shared contracts, database, and UI. **Problem or motivation** An agent can report progress on a task or comment on an authorized task. It cannot send a routine result to its own standing chat with the responsible person. A morning review routine therefore cannot leave a visible digest in that person's chat. **Proposed solution** Add `send_chat_message({body, idempotencyKey})` and `POST /api/agents/me/chat/messages`. The server selects the company, agent, and responsible person from the active run. It saves an attributed comment and audit record in one transaction. The chat shows a source-task link and per-person unread state. **Alternatives considered** A destination parameter on a generic comment tool would expose unnecessary routing authority. A new delivery worker would add another durable delivery path. This change uses a dedicated tool and the existing comment and live-event paths. **Roadmap alignment** This extends the experimental Agent Chat capability in `ROADMAP.md`. The existing `enableAgentChat` setting controls it. Related public work: Refs #13282, Refs #13283, and Refs #14408. Searches for proactive chat and unread chat found no duplicate PR. ## What Changed - Add a focused messaging service shared by the native tool and HTTP route. It checks current run ownership, execution mode, recipient membership, task access, and task privacy. - Reuse the canonical company/agent/person conversation. Save the comment and audit record together. Keep task completion and chat execution separate from delivery. - Add source-task provenance and source-scoped retry keys. Identical retries return the saved receipt. Changed content returns a conflict. - Enforce the conversation's fixed agent at the shared comment-write boundary. Keep normal reply cancellation and session checks. - Add chat unread state, accessible agent dots, aggregate Chat indicators, and visible-message read cutoffs. Refresh through existing live events. - Add the request-key constraint, native tool contracts, documentation, capability maps, stories, and regression coverage. ## Verification - Local delivery/security proof: all 38 proactive-message cases pass. Eight credential-scope regressions and four quota regressions fail against the prior source. The repaired delivery and canonical cross-issue cap suites pass all 49 cases; all 31 OpenAPI tests, server typecheck, and capability-map checks pass. The shared per-run cap covers native and HTTP sends, mixed ordinary mutations, concurrent last-slot contention, and retry/recovery without double charging. - Credential tests preserve the authenticated person and authorizer; reject bridge/test credentials and persisted skill-test runs after task-mode changes; and recheck API-key revocation, scope, and responsible person after destination locking. The earlier delivery/native-authority suites passed all 74 cases before the four quota additions. - Four PostgreSQL contention cases cover native and HTTP sends plus retries during a native chat mutation. All four deadlock against the earlier source and pass with destination-before-source/run locking. Recovery and human-reply delivery enqueue only the human comment; a proactive digest never wakes the chat agent. - Passed 108 companion conversation, native-authority, and OpenAPI tests; 112 runner catalog/workflow-report tests; 47 completion-delivery tests; and 25 project-handoff tests. Focused runner tests cover native tool availability without generic API tools. - All 327 affected UI tests, UI typecheck, token gates, and catalog checks pass. The read hook retries at most three times, respects server retry delay, coalesces only seen cutoffs, recovers on reconnect, and cancels on scope changes. - Real browser journeys with a deterministic process agent verify routine-to-chat delivery, first-chat creation, unread state across reload, the source link, secondary chat navigation, and a follow-up reply referring to the digest. This does not qualify live GitHub retrieval or model output quality. - The Storybook showcase uses production components with deterministic network fixtures. Rendered interactions pass for the landing, ordinary read success, transient read recovery, and persistent failure after bounded retries. Both Chat navigation variants update from two unread chats to one while only Kodi's dot clears. Mobile and light variants were reviewed. The existing Coordinator Recents label contrast finding is unchanged; no Linux visual baseline archive exists. - Current master's independent sandbox migration retains 0418. Regenerated the feature migration as 0419 from the combined schema and retained exactly the newest five snapshots; numbering/safety, replay, and schema-drift checks pass. - Workspace typecheck and build passed before PR preparation; canonical server/UI typechecks passed again on the combined tree. Migration `0419_slippery_impossible_man.sql` passes safety and schema drift checks on disposable PostgreSQL, including interrupted index repair, concurrent migrators, one-time owner read-state backfill, preserved receipts, and two SQL replays. A default five-second local snapshot comparison timed out; a diagnostic 30-second run passed without drift. - Earlier failures are retained in the record: full local `pnpm test:run` and broad shards encountered embedded-PostgreSQL startup, timing, and provider-recovery failures. Thirteen selected external-channel cases pass in isolation on the original and changed sources; an unordered comment-row assertion now explicitly orders both reads. The earlier route registry, native tool count, runner catalog, and accessible Chat badge-name failures were fixed and passed full remote CI on `920b3bb7db`. - Repeated managed-skill server8 failures came from CI's newer synthetic merge: its Cloud guard correctly rejected the old local-disk fixture. Master independently repaired the fixture in #18385; this branch keeps that repair unchanged. All 57 managed-skill and Cloud prerequisite cases pass on the combined tree, and that fixture has no remaining PR diff. - Current reviewed head `dc16f314739a6d977bed21cb1446d0e80a541578`: Greptile 5/5 with no findings, Superagent security assessment passed, advisory Paperclip Review 5/5 with no findings, and zero open review threads. All 55 current-head check runs pass, with five expected skips and the advisory review neutral at 5/5; Snyk also passes. No checks are pending or failing. Protected squash auto-merge is enabled and is waiting for required code-owner approval. A normal exact-head merge was refused by the base-branch policy; no admin bypass was used. The previous head's Superagent quota finding is fixed and covered above. ## Risks - Chat remains company-visible. Delivery rejects a source task with private-task, project, or ancestor restrictions. - Read state uses a comment timestamp cutoff. The server retains database precision and never moves a read receipt backward. - The new unique constraint changes comment query planning. An existing regression now uses an explicit row order. The migration builds the unique index concurrently, then takes a brief table lock to attach it. It uses the existing top-level migration and interrupted-index recovery path. - The upgrade backfills missing chat-owner read-state rows at the latest existing agent comment. Existing read receipts remain intact. New chats can still be unread before the human participates. - Quota observation commits atomically with delivery. A rejected send rolls back its attempted denial audit row and any first-chat creation; the canonical warning remains in server logs, and previously spent quota remains enforced. Identical/conflicting retries and receipt recovery spend no extra slot. - This version delivers in-app only. It adds no external-channel, push, or email delivery. - Local full-suite acceptance remains limited by the failures recorded above. The feature stays behind `enableAgentChat`. ## Model Used OpenAI Codex. PR preparation and CI work used `gpt-6.1-sol` with tool use and code execution. The earlier implementation also used Codex, but its exact model ID was not recorded in the visible session. The context-window size was not provided. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run focused tests locally and they pass; the broad local failures are recorded above - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-30 21:39:07 -05:00
DottaandPaperclip	45a3a92e6d	fix(environments): persist sandbox ownership before creation (#18357) ... ## Thinking Path > - Paperclip manages companies and the agents that do their work. > - Remote execution creates provider resources that need a durable owner. > - The server could create a sandbox before it saved its lease. > - A failed lease write could leave cleanup data only on the old web server disk. > - This change saves a company-scoped operation before creation and transfers ownership atomically. > - Recovery finds the original Daytona resource or records an explicit manual reconciliation outcome. ## Linked Issues or Issue Description **What happened?** A sandbox could exist without a lease after a database failure or company rebind. Failed cleanup recording could then create a local fallback file. Replacing that web server could lose the cleanup reference. **Expected behavior** A failed admission write makes no provider call. An interrupted creation retains a committed operation. Recovery must not create a second sandbox or destroy an attached lease. **Steps to reproduce** 1. Run the disposable PostgreSQL cases in `server/src/__tests__/sandbox-creation-operations.test.ts`. 2. Reject the lease insert after the controlled provider creates its resource. 3. Start a new receiver process with a different empty web disk. It must find the same resource and create one cleanup owner. Related ownership report: Refs #14672. This change addresses new allocations before lease persistence. It does not replace existing lease recovery. ## What Changed - Add an idempotent migration and a small creation-operation table. Retain original company, environment and run identities across deletion. - Commit creation intent before run, ad-hoc lease, and plugin task replacement calls. Fence duplicate requests and ambiguous lease commits. - Retain a known returned task resource ID in the existing operation before attachment. Preserve manual reconciliation and never delete an ambiguously attached resource. - Keep company and run authority checks and atomic lease transfer with the lease owner. - Reuse Daytona names, labels, read-only inspection and claimed cleanup. Keep provider payload handling in the provider. - Retain nonsecret credential identity hashes. Refuse recovery lookup under a changed credential value. - Record manual reconciliation for missing/deleted or explicitly inactive saved credentials, versions, and provider vaults. Keep temporary resolution failures retryable. Never reactivate a disabled credential. - Use transaction signals and concrete deadlines. Failed records back off independently. Manual reconciliation stays durable and quiet. - Remove new orphan-file fallback writes from the covered paths. Keep legacy file replay and its tests for cutover. - Replace obsolete fallback-producer assertions with normal-entrypoint durability tests. Keep cleanup, diagnostics and warm handoff coverage. ## Verification - [Independent current-head verification](https://github.com/paperclipai/paperclip/pull/18357#issuecomment-6534744320) passed 190/190 combined tests, 40/40 incoming TestOps tests, full workspace typecheck, and build. PR head `958af986130f25e136065ad30d1fdd843c46255c` has tree `e6c3e5b02182d5941a70ccf5bf55638df3c2e28d`, identical to tested combined commit `b9d7a9c2e9b30f0153685fb24a5f70b56132201f`. Real PostgreSQL, compiled Rust Runner and controlled object providers were used; external-S3 integration remains outside this local proof. - Current head `958af986130f25e136065ad30d1fdd843c46255c` normally merges master `8595efc20bda3ce20a9fbbf34a5d156a6fcf6d57`. The sole conflict was the maintenance test: a parameterized case now preserves both legacy-local `local_storage` and valid shared-S3 `provider_mismatch` checks, including the parent local receipt, exact version identity, missing-snapshot/no-seed refusal, and unchanged persisted row. The three master TestOps files remain intact. No production, schema, migration, or package changes were made after the fully qualified prior head `0b4d05505e`. Independent review approved the resolution; the full managed-skill-content file and Cloud guard controls pass 58/58 (105.11 seconds). [Required PR CI passed on this exact merge head, first attempt](https://github.com/paperclipai/paperclip/actions/runs/41136987412): 54 successful checks and three intended skips. The additional Paperclip review is neutral at 4/5; two external Superagent checks (Contributor trust and Security Scan) remain in progress with zero annotations and no assessment, so they are not passing scan evidence. Greptile reviewed exact head `958af986130f25e136065ad30d1fdd843c46255c` at 5/5; the final thread audit has zero unresolved threads. All completed evidence below retains its recorded revision scope. The additional Paperclip Review on `958af98613` is neutral at 4/5 with a Ship verdict and no must-fix or should-fix item. Its optional observation is that a generic create rejection remains pending/manual even when an operator believes allocation did not occur. This change preserves uncertainty because the generic create-error contract does not prove provider absence; no new error classification or provider-specific compensation was added. - [Independent final-source verification](https://github.com/paperclipai/paperclip/pull/18357#issuecomment-6534328247) passed all 189 real-PostgreSQL/Runner and controlled-fixture cases, full workspace typecheck, and build. The integration commit `c8411a8528386f4824b340ec5fdaaed1efb9ea69` has the same source tree as final PR head `0b4d05505e` (tree `bda65efc14b4c904d0f589154db77bb160641c8c`). Controlled object-provider coverage passed; the separately guarded external-S3 suite was not run because the bounded local MinIO pull was unavailable. This includes the two final compatibility fixes. - The first final-head CI attempt exposed one E2E timing failure in `disconnect-write-recovery.spec.ts:181`: the title stayed unchanged through the 15-second session-recovery poll. The same original case passed in 13.8 seconds on immediately prior head `7ec06f77b7`, and all UI/session/E2E source is identical across those heads. The failure log and CI artifacts are retained; no cause is claimed. One failed-job-only retry is authorized on this evidence, without changing a timeout, assertion, or production behavior. [The single failed-job retry completed successfully](https://github.com/paperclipai/paperclip/actions/runs/41133619710/attempts/2): all 35 E2E shard cases passed (6.6 minutes), including the original session-recovery case in 14.0 seconds. The initial failure remains disclosed and its cause remains unproven. - Final head `0b4d05505ee0aa72f2981cdff74761406960ec73` adds two independently reviewed integration fixes after the complete 7ec CI matrix exposed two deterministic failures. Server 9/12 failed legacy local-storage maintenance because the CLI reached the new Cloud server startup guard; server 5/12 found the Daytona package version did not match its bumped manifest. The failed run is retained at https://github.com/paperclipai/paperclip/actions/runs/41131204203. It is not passing evidence and was not blindly retried. - Maintenance now constructs the existing explicit storage dependency after loading the required persisted Cloud snapshot, and passes it to both maintenance owners. It can verify legacy local storage before provider cutover while normal Cloud server startup remains guarded. The original case reproduced red locally, then the complete managed-skill-content and managed-cloud-prerequisites files passed 57/57 (32.05 seconds), including missing-snapshot refusal, unchanged stored configuration, and existing server guard controls. Daytona package version now matches manifest 0.1.10; the complete bundled package identity file passed 14/14 (3.98 seconds), and explicit manifest/lifecycle controls passed 2/2 (328 intentionally filtered; 3.42 seconds). An initial workspace-filter command matched no project and is not counted as pass evidence. The final diff changes no sandbox runtime or schema behavior. [Full CI is green on this exact final head](https://github.com/paperclipai/paperclip/actions/runs/41133619710/attempts/2): 56 successful checks, three intended skips, one additional incomplete/neutral Paperclip Review, and no pending or failed checks. The neutral review is not a passing assessment. [Greptile reviewed the exact final head at 5/5](https://github.com/paperclipai/paperclip/pull/18357#issuecomment-6529396969), with no new actionable issues and all review threads resolved. - Final combined head `7ec06f77b7c14a745c569d18401f16df3d26b626` includes master managed-skills migration 0417 and shared-storage prerequisites from `198218bf55` through normal merges. Sandbox creation moves to generated `0418_curved_lady_mastermind.sql`; its idempotent SQL is byte-for-byte unchanged. The regenerated 0418 snapshot contains both sandbox creation operations and the master skill mutation receipts, and points to the master 0417 snapshot. Master SQL and journal history remain intact. Exactly five snapshots remain, 0414 through 0418. The only sandbox-specific changes since the approved credential policy are migration metadata/number and the matching test/document references; the sandbox runtime files are unchanged. - [Independent final combined verification](https://github.com/paperclipai/paperclip/pull/18357#issuecomment-6533960026) passed on integration revision `e6f05b4cf0cd`, containing final sandbox head `7ec06f77b7` and actual master `198218bf55`: migration/declaration checks, all 158 real-PostgreSQL/Runner and controlled-fixture cases (251 seconds), full workspace typecheck (81 seconds), and build (35 seconds). - Final combined migration proof: fresh real PostgreSQL has both tables. A separate original-0417 sandbox table with a retained pending row survives two applications of the renamed 0418 SQL unchanged, with the expected primary/index and foreign-key structure. Migration numbering/safety checks pass. The normal runtime migration reapply case passes 1/1 (20 intentionally filtered cases; 46.69 seconds). The first temporary qualification harness stopped before any database assertion because its external `.ts` file selected CommonJS; the `.mts` harness corrected that setup and passed. Independent review approved the exact metadata and reference diff. Earlier full suite and live-provider results below retain their stated revision scope. - Credential-policy head `c606d473b03709f27577a55a1dfc0b0d3b4359fd` handles the remaining inactive-credential review warning. The existing boundary accepts only concrete secret-owner 422 codes and exact no-details disabled/coming-soon vault messages. Unknown 422, authorization errors, provider wrappers, and temporary database/provider failures still propagate. Independent source review approved this three-file correction. No generic resolver, schema, provider protocol, retry cap, or activation behavior changed. - Creation/cleanup qualification at `c606d473b0`: all 39 cases pass against real PostgreSQL (81.27 seconds). The new cases use actual disabled/archived saved secrets, a valid disabled version, and provider vaults created ready before normal API updates disable them or mark them coming soon. Each remains manual through restart/repeated scans, with zero provider lookup and no retry deadline. The independent plugin idle blocker remains intact. The temporary 503 control retains retry ownership and later recovers one cleanup owner. Before this correction, all five inactive-state cases remained pending; that failed evidence is retained. The prior 18-case known-ID task proof below belongs to `237144fcf6`, whose helper and task path are unchanged by this correction. - Known-ID head `237144fcf69a249c0e0310563428c0f55ed6d55c` also addresses the independent task-replacement reliability warning. The existing creation operation now saves only the known nonsecret returned resource ID before expiry validation and attachment. The write is scoped to operation/company/original environment and allows only a missing or matching ID. It changes no ownership state and copies no resolved configuration, credentials, or provider payload. Independent source review approved this four-file fix. - The complete real-PostgreSQL task suite passes 18/18 (9.52 seconds). Rejected attachments retain the ID through manual reconciliation and repeated scans. A real committed attachment followed by an injected lost response retains the same active lease and attached operation, with no release or second create. Same-ID retries work; conflicting IDs and foreign companies cannot change it. The initial three regression cases failed because the ID was absent, before the fix. - The shipped Daytona manifest does not declare task support, so it cannot enter this generic replacement path. The dispatcher requires both declared task support and an environmentTask worker method. Generic drivers without creation lookup still use manual reconciliation, with a known returned ID retained when the database write can commit. No automatic lookup capability or unconditional compensation was added. - Previous boundary-fix head `8ba77def151ea85eeae2db7693254db7f87673b0` fixes the fresh review finding about missing credentials. Only known secret-owner 404 results at the recovery secret-resolution boundary select the existing manual outcome. Provider inspection and transient database/provider errors remain retryable. Independent source review approved this change. - Secret-boundary focused acceptance at `8ba77def15`: all 34 cases pass against isolated real PostgreSQL. The complete creation suite passes 16/16 (100.75 seconds); the complete cleanup coordinator suite passes 18/18 (99.83 seconds). The new cases use normal saved-secret creation and deletion, confirm zero provider lookup, restart/repeated scans, no automatic deadline, preserved independent plugin idle blocking, and no additional idle blocker after the controlled worker supplies its quiet proof. A temporary 503 resolution failure preserves pending ownership and later recovers one cleanup owner. No additional live provider resource was created. - Failed attempts remain part of the evidence. The initial red run reproduced the pending-operation bug and also exposed a numeric-deadline test harness mistake, which was corrected. A later combined run reported an existing replacement-receiver failure and a new idle-fixture assertion failure; it was interrupted while the next test file remained in imports. An isolated diagnostic confirmed that the manual state was correct but the installed fixture plugin correctly blocked sleep without its independent quiet proof. The corrected test retains that blocker assertion before supplying the controlled worker witness. The unchanged replacement-receiver case passes in the final complete 16-case run; its earlier failure is not counted as a pass or assigned a proven cause. No timeout or production idle guard was relaxed. - Greptile reviewed previous combined head `7ec06f77b7c14a745c569d18401f16df3d26b626` at 5/5, with no unresolved review threads. Its CI produced the two concrete integration failures addressed above. The earlier CI and live evidence below remain historical evidence, not a claim that the current full gates have completed. - Master integration update: merged `dbff3747b8` and then latest master `76fde891cc` without rewriting branch history. Only `doc/DATABASE.md` conflicted; the sandbox ownership, object-backed run evidence, and cloud configuration sections all remain. The master merges changed no sandbox implementation, migration, or provider code. Migration numbering/safety checks pass and exactly five schema snapshots remain. At merge head `f5d23d4a59828835d01c150f83fa2645fb2d3bec`, the two focused creation/coordinator suites pass all 32 cases against isolated real PostgreSQL (64.57 seconds). Those merge-head checks precede the missing-credential fix below. The earlier live Daytona proof still covers the unchanged normal creation/lookup/teardown path; the new missing-credential branch is qualified with real PostgreSQL and controlled provider hooks. The optional Superagent Security Scan was inconclusive on prior head `7ec06f77b7`: its pinned PR merge-base checkout failed or timed out, with a neutral conclusion and zero annotations. An earlier scan could not start within 120 seconds; a bounded rerun request returned HTTP 404. These scanner failures are not passing security-scan evidence. On final head `0b4d05505e`, the additional Paperclip Review check is neutral: its assigned review execution did not complete and produced no validated assessment. Fresh Greptile 5/5 and independent source review are separate evidence. Previous-head required CI, independent review, and the live Daytona qualification below passed. - [Complete previous-head CI](https://github.com/paperclipai/paperclip/actions/runs/41105726052) passed at `0b5cbb763ab8faa25aa0ff1d8a405cdc0d3db409`: 53 successful checks and three intended skips, including typecheck, full tests, build and E2E. Greptile is 5/5 on this head and both original findings are resolved. - Initial head: 200 PostgreSQL runtime, creation and coordinator tests passed. The corrected head also passes all 32 creation and coordinator tests, including deletion before/during lookup, a failed lookup after deletion, restart, settled polling and actual idle-safety checks. Cases cover failed admission, failed lease writes, concurrent recovery, lost provider replies, ambiguous transfer retries, company rebind, environment deletion, stopped runs, lookup backoff, restart, drain and settled SQL quiet. - Separate receiver processes: passed. A controlled HTTP provider retains the resource while three independent receiver processes use two empty web disks. Recovery creates one cleanup owner and never repeats creation. - Fresh PostgreSQL migration and two additional applications: passed. The pending creation row survives unchanged. - Server TypeScript and SDK/shared build checks pass after the corrections. Migration numbering/safety checks passed. Exactly five schema snapshots remain. - Daytona adapter: all 330 tests passed, including stable-name lookup, ownership checks, deletion and the updated manifest version. An earlier run exposed the version expectation and it was corrected. Previous-head CI passed. - Live Daytona acceptance passed on `0b5cbb763a`: isolated real PostgreSQL, normal runtime acquisition through independent receiver processes, actual Daytona plugin/SDK 0.203.0, one disposable Ubuntu 24.04 sandbox (1 CPU / 1 GiB RAM / 1 GiB disk). A forced lease insert failure retained the committed operation; a fresh receiver with empty disk found the same sandbox, repeated recovery retained one cleanup owner, and the actual claimed cleanup sweep expired the lease and resolved the operation. Independent SDK lookup returned typed not-found; ordinary recorded-ID inspection returned destroyed. This successful attempt made one create, one recovery lookup, and one teardown. Two earlier failed harness/provider-confirmation attempts are disclosed in the [live acceptance record](https://github.com/paperclipai/paperclip/pull/18357#issuecomment-6530313054). The coordinator independently queried all three exact resource IDs through the SDK and confirmed typed not-found for each. - Complete CI-affected heartbeat/plugin warm-task suites passed 21/21 after test corrections. An unchanged workspace exposure case passed in isolation after the prior CI shard reported an unhandled readiness rejection. Complete previous-head CI and refreshed review passed. ## Risks - Deleted companies retain an explicit manual reconciliation outcome. Recovery does not retry missing credentials or insert a lease for a deleted company. - Only Daytona declares automatic creation lookup. Other uncertain providers retain `needs_reconciliation`. A missing creation name alone cannot prove that a late allocation will never appear. - Pending operations use the existing process-local signal and startup recovery model. This does not add cross-replica wake delivery or prove deployed sleep. - Legacy direct provider probes and custom-image setup use separate lifecycles. They are outside this replacement of the run-lease orphan-file fallback. The normal Test path that acquires a runtime lease is covered. - Existing orphan files still require the separate cutover inventory and settlement. This change does not delete them. - The schema change is additive. The new SQL can be reapplied. Historical SQL and journal entries are preserved; only the oldest generated snapshot is pruned. ## Model Used OpenAI `gpt-6.1-sol`, with tool use, code execution and repository review. The harness did not report the context-window size. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge The required branch status checks (`ci / verify`, `ci / e2e`) and all test/build jobs passed on this head. The non-required Superagent Contributor trust and Security Scan checks are still running without findings; they are not claimed as passes. No required check or branch rule is overridden. --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-30 17:38:23 -05:00
DottaandPaperclip	dbff3747b8	feat(server): persist run logs and provider traces in S3 (#18327) ... ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Operators use run logs and restricted provider traces to inspect agent work. > - Local log and trace files depend on the web server's persistent volume. > - That dependency prevents overlapping volume-backed Railway deployments. > - This PR reuses the instance S3 store for batched log and trace payloads with conditional publication. > - Existing Postgres rows retain their contracts; native export recovery reuses events already committed before Runner acknowledgement. > - S3-configured servers automatically copy and verify retained history before a later deployment cutover. ## Linked Issues or Issue Description **Subsystem affected** Server run logs, restricted provider traces, storage providers, and migration tooling. **Problem or motivation** Replacing the web server and its disk must preserve committed log output and retained traces. The current S3 mirror can repeatedly upload a growing file. Moving those payloads into Postgres would add database writes, WAL, replication, and backup work. **Proposed solution** Reuse the existing instance storage configuration, S3-compatible provider and credential chain. Store new run logs under run-logs/ and opted-in raw traces under provider-traces/, below the existing prefix. Cloud keeps its existing bucket and bucket-scoped credentials per stack. Add no new configuration switches. Store immutable payload segments and bounded binary range indexes directly in S3. Publish each batch with an ETag-conditional head. Keep existing database ownership and lifecycle records. Recover canonical native exports from their existing validated control event source, checkpointing export progress in S3. Add no new payload writes to Postgres. Preserve local defaults and migrate settled history with verified byte counts and digests. **Alternatives considered** Postgres payload chunks add control-plane load. Repeated whole-file mirrors amplify transfer work. The first index prototype left superseded index nodes; the final binary index keeps all normally published nodes reachable. **Roadmap alignment** This is a storage prerequisite for replacing the main web/API server. It does not enable deployment overlap, detach a volume, or change native Runner protocol acknowledgements. The maintainer approved this implementation scope. ROADMAP.md has no duplicate implementation item. Related PR: #16770 improves the existing in-flight mirror. This PR preserves that legacy backend and uses the existing instance S3 profile for new journals. ## What Changed - Automatically select S3 segments for new logs and opted-in traces when instance file storage uses S3. Reuse bucket, endpoint, region, prefix, path style and credentials. Remove separate backend switches. Keep local-disk instances local. - Share the existing storage configuration resolver with product files. Preserve config-file settings, environment precedence and the existing root prefix. Keep pre-existing run-log mirror settings for legacy history. - Add bounded buffering, conditional ownership fencing, immutable range reads, stable byte offsets, and completion hashing. - Dispatch all existing log consumers through the recorded backend. Coalesce output progress writes and publish live log messages after storage receipts. - Recover interrupted canonical native exports from their existing durable source. Exclude separate credential, cleanup, and reprojection records. Replay missing callback ranges and deduplicate late delivery. Repair settled archives after controller lease expiry. Bound shared repair work and stop it when all readers cancel. Serve the published prefix when best-effort repair fails. - Add encrypted optional trace channels, replacement reads, durable deletion tombstones, and deadline-driven local/external expiry cleanup independently of heartbeat scheduling. Stream historical source and remote verification. Propagate worker cancellation through trace open, conditional-write probing, upload, restore and reads. Fence deletion even before the first object head exists; abort and drain owned captures. - Retry transient storage errors, distinguish 409 from failed preconditions, and backpressure bounded log admission. Track interrupted trace imports explicitly so ordinary local deletion stays independent of S3. - Automatically migrate retained history through the existing delivery coordinator. Process one log and one trace per batch. Retry unresolved history with backoff and stop scans after completion. Keep the inventory/import command as optional diagnosis and repair. Verify source and remote bytes before switching references. Verify finalized native size and digest before setting its export cursor. Require ordered source coverage when completeness metadata is missing. Preserve original trace expiry. Block active, missing, corrupt, and unproven sources. - Preserve identity and run-secret redaction in live and recovered native logs. Register runtime log redaction secrets once through the existing encrypted registry. Keep agent private keys in their existing owner. - Add storage, migration, retention, UTF-8, and route-privacy coverage, plus operating documentation and qualification tooling. - Add no schema, payload table, per-record SQL, production dependency, or lockfile change. ## Verification - Final fixes at `b3a44c898e` passed all 116 selected startup, retention, attribution and cancellation controls. The disabled-scheduler cleanup and concurrent-repair defects reproduced red before the fixes. A timed-out repair still prevents later storage reads. - The merged source passed 124 storage and real-Postgres Cloud configuration tests. These include automatic history migration, existing environment/file vault keys, source-directory removal, five real-SDK stalled-request cancellation cases, shared capability-probe cancellation and multi-chunk trace ordering. Saved Cloud S3 settings work after the legacy config file is gone. - Workspace typecheck and full build passed at the merged parent `19f702d780`. Server typecheck and build passed again at `b3a44c898e`. - Actual app acceptance: finish a process-agent run through the normal API, stage its retained local-file input, then restart. Automatic migration reports one migrated item and zero blockers. Remove the original web home and restart at `b3a44c898e` with an empty home, the existing S3 profile and the existing vault key file. The normal log API preserves all five producer lines and exactly 788 bytes, with SHA-256 `74d9ae469da28bfe89b9b50a0e132aec24fe9e6d686496ed5e4ffa6167151036`. No log-specific storage settings are present. - Actual expiry acceptance: with heartbeat scheduling disabled, a trace remains unexpired after startup and later reaches its fixture deadline. The worker marks the row deleted and tombstones both S3 channel heads. The retained run log stays byte-identical. The process fixture emits no provider protocol frames, so nonempty encrypted payloads are qualified separately through the real SDK round trips. - Isolation tests use identical run identities in two stack buckets. Cleanup in one existing prefix leaves another prefix, another company and product files intact. Read-only Cloud source inspection confirms a bucket and bucket-scoped credentials per stack. Four existing Cloud storage environment-contract tests passed. No Cloud provisioning changed and no new live vendor permission probe was performed. - Earlier qualification passed 1,014 affected storage/native tests and 27 privacy-route tests with isolated Docker Postgres. An abrupt process test commits 1,000 records, receives receipts, dies by SIGKILL and loses its directory; another process reads every byte and continues. The real Rust Runner experiment acknowledges 32 records while the export cursor is zero, then continues the same Runner PID after controller loss. All 64 records export once with exactly 64 existing control rows. Repeated snapshot/Stop commands completed in 162/81 ms. - Emulator workload: 1,000 burst records used two batch PUTs. Eight steady streams produced 240 records with 104 conditional PUTs and 72 GETs over 6.9 seconds. These are synthetic operation counts, not fleet sizing or provider prices. - Failure evidence is retained. Compact native events over 64 KiB, missing file-key support, disabled-scheduler retention and repair failure handling all reproduced before their fixes. Fixture repairs addressed cold module setup, localhost/IPC permissions, the S3 bucket-name limit and a mode-0700 crash-test directory. Full local `pnpm test:run` was stopped after host PostgreSQL semaphore exhaustion; affected suites used isolated Docker databases instead. Native package library symlinks were restored with the package's standard hydration helper. - The `19f702d780` browser session-recovery case timed out while saving a task title. All eight browser shards passed on `b3a44c898e`, including that case, with no UI behavior or assertion change. Fresh-head CI passed at `b3a44c898e`: 55 successful checks, three skipped checks and one neutral check. The branch is conflict-free. - Map and module-boundary checks passed. Current-head Greptile is 5/5 with zero unresolved review threads. Reproduce the opt-in storage suites with `PAPERCLIP_LOG_TEST_S3_ENDPOINT` and a dedicated `PAPERCLIP_RUN_EVIDENCE_MIGRATION_DATABASE_URL` ending in `_test`. See `doc/run-evidence-storage.md` for operating limits, automatic migration, optional diagnostics and rollout qualification. ## Risks - Keep the existing per-stack bucket, prefix and vault key stable across replacements. Relocating that storage is a separate whole-instance operation. - This release automatically changes new log storage for existing S3-configured instances. Local-disk instances remain local. Canonical native source replay is qualified with a deterministic real Runner; actual remote execution and production-provider qualification remain rollout gates. Generic server-only diagnostics and optional raw trace tails without a surviving source can be incomplete after a crash. This does not establish full zero-downtime deployment. - Before deploying this release, qualify the actual S3 provider. It must enforce conditional writes and pass read, version, deletion, workload, and latency qualification. A capability probe rejects providers which ignore preconditions. Moto is emulator evidence only. - Dirty output is bounded and unconfirmed until S3 publication. Storage failure leaves persistence incomplete while task results and usage can settle. - Trace expiry is not yet represented by Cloud's external wake contract. Outstanding trace deadlines conservatively block sleep. - Automatic history copying requires the original source volume. Keep it until all retained resources pass verified import and clean-filesystem reads. Stop old binaries from creating new local-file runs. Missing or corrupt history remains blocked and visible in server logs. Rollback requires a compatible reader against the same external state. Ordinary object deletion does not erase retained historical object versions or backups. ## Model Used OpenAI Codex, `gpt-6.1-sol`, with reasoning, tool use, code execution, and browser verification. The runtime did not expose a context-window size. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-30 15:17:35 -05:00