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| Author | SHA1 | Message | Date | |
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 DottaandPaperclip
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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> |
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DottaandPaperclip
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0e15c92073 |
feat(skills): make managed content independent of web-server disk (#18334)
## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Agents use installed skills and exact version pins during execution. > - Managed skills still depended on mutable directories on the web server. > - A replacement server could lose acknowledged edits or remove an unassigned skill whose directory was absent. > - This pull request makes immutable versions the authority for managed content and installed repository reads. > - The server can rebuild delivery files from durable content after replacement. > - This establishes skills readiness for ephemeral web servers. General server draining and workspace recovery remain separate work. ## Linked Issues or Issue Description **Subsystem affected** Skills services, shared contracts, database receipts, Skill Studio, and runtime delivery. **Problem or motivation** A fresh web server must discover, read, edit, and deliver protected installed skills using the same database, object storage, secrets, and supported application artifacts. It must not need its predecessor's files or process memory. **Proposed solution** Use `managed` ownership with a null source locator. Read installed content by immutable version. Prepare packages before a short publication transaction. Persist execution selections before materialization. Recover exact pinned runtime assets and reject deletion while active or recovering pins exist. **Alternatives considered** Reconstructing a mutable installed directory preserves the old source-of-truth ambiguity. Permanent dual writes create two competing authorities. This change uses one managed model after a bounded legacy conversion. **Roadmap alignment** This improves the existing Skills Manager, Studio, version history, and Cloud execution capabilities. The maintainer supplied the implementation contract. This does not add a separate skills product or deploy fleet changes. Related work: #18082 supplies immutable package storage. #17273 addresses edits outside the API for linked local skills; this PR keeps that source category separate. #2648 is a closed earlier ephemeral-filesystem proposal. ## What Changed - Add managed ownership and focused content publication and execution materialization modules. Keep the archive format and package storage tables. - Publish managed create, save, delete, fork, rename, restore, and catalog content with version checks. Add durable create receipts. Preserve file-save receipt responses. - Return file version identities. Keep Studio drafts after a conflict and provide an explicit reload action. A delayed reload cannot overwrite newer typing or navigation. - Persist exact runtime selections, including empty selections. Rebuild pinned assets and verify their admitted digests on a replacement server. - Preserve source access on forks and disconnected copies. Keep the existing workspace policy category for managed skills. - Add bounded conversion, eligibility, and independent verification phases. Load persisted Cloud configuration in the standalone CLI without seeding or changing it. Reject partial current versions against installed inventories; recover only complete saved content or the exact source. Document storage migration blockers and the compatible rollback floor. - Add separate-process PostgreSQL/S3 qualification and update domain, retention, policy, and UI regressions. - Pass the plugin worker manager into Studio execution, admit restricted `skill_test` mode through native Runner contracts, and preserve admitted scope across native and REST tools. Native tests cannot create ordinary tasks, browse company data, or use external tools. - Select the exact durable Studio revision even when unassigned or Beta skills is off. Persist Studio output and audit atomically with native task completion, preserving the result on replay. ## Verification - Final revision `13e8af480b88ba6fea5737bac4bd81104d604792` passed full CI: all 49 workflow jobs completed successfully ([run 41127396098](https://github.com/paperclipai/paperclip/actions/runs/41127396098)). This includes typecheck, test suites, Runner checks, browser checks and build. Greptile review 15 is 5/5 on that same revision, with zero unresolved threads. The PR is ready for review. - Local workspace typecheck and build passed after integrating master. Focused checks passed: 33 execution/completion cases, 52 Runner HTTP cases, 16 managed-content cases, 17 Studio cases, the new real-process CLI regression, map checks and UI token gates. The CLI regression proves inspection does not seed missing Cloud configuration. Server typecheck passed after that fix. - The independent-process PostgreSQL/S3 matrix passed through normal HTTP skill routes. It covers A → B → C replacement, lost commit responses, upload crashes, concurrent saves, binary contents and executable delivery. Metadata listing and warm selected delivery retain zero object downloads. Local timing measurements are recorded; they do not establish hosted latency. - Hosted A → B → C passed on the owned disposable test tenant with external Postgres, S3 and a real remote Paperclip Computer. Predecessor temporary homes were absent. C read and executed B's acknowledged managed save. New runs used repository v1 while v2 was installed. Hashes matched an independently checked exact upstream commit. - Compatible image rollback to `6518b323` passed. Studio retained the unassigned fork's C save. A fresh remote run executed the newer managed content and historical repository pin. The actual shell event confirmed expected hashes, stdout, exit 0 and mode 0555. - Runtime candidate `9200e3fcb4` deployed successfully ([Cloud run 41124147876](https://github.com/paperclipai/paperclip-cloud/actions/runs/41124147876)). The final Studio test delivered only the unassigned fork's exact v3, executed its script and persisted a successful output snapshot. Independent command-event inspection confirmed all three hashes, stdout, exit 0 and mode 0555. All 14 installations were version-backed. Independent verification checked all 25 versions: 23 remote objects, two bundled database snapshots, zero blockers. - The deployed image is `9200e3fcb4`. Later master integration, the client-only delayed-reload draft guard and the CLI bootstrap have separate automated proof. The CLI bootstrap was also exercised against the tenant's stored configuration and storage through the same read-only services. This PR does not claim that the deployed image is the final PR revision. - Live Studio checks exposed worker wiring, admission, access scope, exact selection and completion-publication gaps. They are fixed. Failed attempts remain in the evidence. The full local suite exceeded 80 minutes under host contention and was stopped. Later combined/isolated local attempts also timed out; they are not counted as passes. Full CI covers the integrated suites. Earlier CI found an obsolete restart-scope fixture, which was corrected and passed all 52 HTTP cases. - Reproduction and migration: [`doc/skill-ephemeral-web-servers.md`](doc/skill-ephemeral-web-servers.md). Source revisions, deployments, versions, run IDs, hashes and failure history: [`doc/plans/2026-10-30-ephemeral-web-skills.md`](doc/plans/2026-10-30-ephemeral-web-skills.md). ## Risks - Legacy conversion requires stopped admission and retired filesystem-authoritative writers. Pre-conversion binaries are not supported rollback targets afterward. - Cloud readiness requires remote object storage. Local provider receipts and provider mismatches remain blockers until objects are copied and verified. - Linked local sources retain filesystem semantics and are outside the cloud guarantee. - Cold reads still fetch the existing archive format. Warm runtime preparation retains the verified-cache path. - Bundled reconciliation preserves an installed head. Existing release snapshots remain selectable. An older server must not replace a newer head with its shipped files. - No production volumes, fleet defaults, or general deployment coordination change in this PR. ## Model Used OpenAI Codex, GPT-6 family, with reasoning, repository tools, code execution, and browser use. The exact backend model ID and context-window size are not exposed in this session. No subagents were 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 --------- Co-authored-by: Paperclip <noreply@paperclip.ing> |
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DottaandPaperclip
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f1911a4c53 |
perf(skills): move repository packages out of Postgres (#18082)
<!-- entire-trail-link-start --> https://entire.com/gh/paperclipai/-/trails/205/changes/paperclip/205 <!-- entire-trail-link-end --> ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Agents receive selected company skills before each turn. > - Imported skills can need files from the whole source repository. > - The current path stores those files in Postgres and reads large JSON payloads during preparation. > - This pull request stores verified packages in the configured file or object store and keeps preparation queries small. > - It also converts old rows automatically and restores missing files from the exact saved commit. > - The result reduces database traffic while preserving skill versions and repository dependencies. ## Linked Issues or Issue Description **What existing behavior does this improve?** Company skill import, version storage, and preparation before agent turns. **Current behavior** Repository snapshot bodies live in JSONB. Skill preparation can read those bodies again even when the files already exist on disk. Historical packages and native assets also need a bounded cleanup path. **Proposed behavior** Store package archives and manifests through the existing storage service. Keep version identities, receipts, hashes, and recovery metadata in Postgres. Convert legacy rows after the stored package passes read-back verification. A missing package can use legacy bytes or its exact Git commit under current repository authorization. No separate data-migration command is required. **Reason and benefit** The warm path sends no repository bodies through SQL and reads no object bytes. Cleanup runs through the existing deadline coordinator. Current versions, active runs, explicit pins, and authored content retain their protection. **Breaking changes** The normal application schema upgrade is required. Single-version and skill-file responses keep their existing shape. Version lists, current-version summaries, and test-run version summaries now contain file names and kinds without file bodies. Diff and restore fetch selected versions through the existing single-version endpoint. Older server builds must not write after conversion unless they support the new package format. The storage override and rollback limits are documented in `doc/skill-package-storage.md`. **Additional context** Related work: #15731 preserves repository dependencies; #17923 changes version-cache scheduling; #18080 changes delivery to remote Codex homes. This change owns package persistence, acquisition, and expiry. It does not replace those delivery or scheduler changes. ## What Changed - Add company-scoped archive receipts, exact-commit recovery recipes, migration deadlines, and a durable object-deletion queue. - Add bounded archive upload, read-back verification, extraction, concurrent request coalescing, and verified local caches. - Convert old snapshots and versions automatically. Keep legacy bytes when verification fails. - Recover missing files through current source authorization and the original commit. Validate repository identity, file hashes, modes, and the aggregate hash. - Expire unused recoverable Git packages and native assets after 30 days. Preserve active pins and the durable copy of authored or unproven content. - Keep warm preparation queries metadata-only. Bound file digest caches and avoid repeated body hashing when file identities are unchanged. - Extend the existing storage contract with cancellation. Register package work with the existing coordinator. Optional conversion retries retain the original bytes and may wait for ingress without blocking sleep. - Add regression tests, operating guidance, a deep trace, benchmark receipts, and an optional maintenance command. ## Verification ### Final master integration and review repair — October 29, 2026 Current head: `a6065424249e763dfeac37161f1b52a9f25bd9b7`. Commit `f8bbdd3dbd` resolves the conflicts with master `76a796e964`; the final two commits repair the Apex deletion findings below. - Keep both package-maintenance and version-retention notifications in their write transactions. - Keep the shared run-pin predicate and master's controller-lease deadline metadata. Package expiry reads the updated protected-version result. - Preserve every master migration entry. Generate migration **0415 (`0415_zippy_zemo.sql`)** after master's 0414. Its skill SQL is byte-for-byte unchanged from the previously tested idempotent migration. Retain only the five newest schema snapshots. Migration numbering and safety checks pass. - Repair failed file/folder deletion: preserve a complete temporary subtree until transaction commit, restore on upload or SQL failure, and restore callback failures before releasing the mutation lock. Both PostgreSQL regressions reproduced missing files before the fix and now pass. They cover binary data, executable permissions, empty folders, unlisted files, unchanged database/version rows, successful retry after upload-claim expiry, and historical reads. - Reconcile lost commit replies under the same advisory and row locks. Check the saved version and source identity before restoring. Keep committed deletions intact and preserve backups when the database outcome is unknown or a newer edit exists. Four real-PostgreSQL outcome tests pass; the prior code failed three of them. - Full workspace typecheck and production build pass on the final commit. All **204** focused PostgreSQL package/cache/retention/authoring and filesystem-boundary tests pass, with none skipped. - Apex review **18 passes 5/5**, with zero new comments on the exact final head. All **34** review conversations are resolved. - [Final-head CI](https://github.com/paperclipai/paperclip/actions/runs/40914116508) completes successfully on attempt 2. The head has **55 successful checks**, two neutral reports, two skipped checks, and a successful Snyk status. No checks are pending or failing. All eight browser shards pass. - Runner Vitest 2/2 timed out once in the unchanged ACPX controller-replacement fixture. The same job passed on the preceding commit. One unchanged CI retry passes all five ACPX recovery cases, **2,253** Runner package cases and **126** native server integration cases; their standard one and five skips remain. The initial timeout's root cause is not established. Local diagnosis also hit the fixture's eight-second session.open timeout with an authenticated Runner; no local Runner pass is claimed. - Both full local `pnpm test:run` attempts were stopped when Apex identified deletion defects and source repair became necessary; neither is claimed as a passing full local run. The final **204** focused tests, full workspace typecheck, and production build pass. Full-suite acceptance uses the final-head CI jobs. The superseded merge-head CI included runners terminated by shutdown signals; each source repair started a new full run. - Auto-merge is enabled for squash merge. The final head is conflict-free and all checks pass. GitHub's active master ruleset still requires a code-owner approval for the dependency files. The existing review requests are with `devinfoley`, `nickyleach`, and `forgottendev`; no policy bypass was used. - The earlier hosted stress and full native receipts below remain tied to `a2e597d800`; they are not relabeled as a deployment of this final integration. The earlier local PostgreSQL startup failure remains recorded below; PostgreSQL ran successfully for this integration verification. ### Full native skill execution — October 29, 2026 The full native-agent acceptance gap is closed on candidate `a2e597d800eb989d565780e7aa947d5368676444`. Two qualifying native turns used OpenAI API / `gpt-5.4-mini` in real Daytona sandboxes, on the same disposable hosted TEST tenant as the stress test. A follow-up on the same task consumed a newly saved skill version. The task text asked for the assigned skill workflow. It did not contain the proof nonce or expected receipt. The assigned authored skill contained a Python verifier and a random package-local nonce. The agent read the actual installed skill files and executed that verifier against the imported, automatically converted 1,360-file repository package. It checked the repository file count and reference/binary bytes, and directly executed the repository's executable probe. Independent verification matched the emitted JSON to the nonce and expected byte hashes. The agent persisted the same receipt as its task response; native finalization committed, workspace finalization succeeded, and task state became Done. | Qualifying turn | End-to-end run time | Recorded skills.prepare | Repository files | Binary hex | Shell receipt SHA-256 | |---|---:|---:|---:|---|---| | Initial task | 47.881 s | 1822 ms | 1360 | `00ff07800a` | `a1deb30dc095f2306c7aa9cc5ec396da12c68961cf5b809f4d7c20f7fc68493b` | | Corrected follow-up, new nonce/version | 37.974 s | 377 ms | 1360 | `00ff07800a` | `dbcdc33fa1376b4edc136feae1cdf770560a73292467e93619efdda20e4282a7` | Both successful shell receipts reported `probe: STRESS18082` and `assetSha256: e8ea7a2f15f7bb3b332a46adbef848465884c8996595aa234748befd544d1f3a`. Their proof nonces, selected version IDs and receipt hashes differed, and both ran on the same task. These are observed timings, not latency SLOs; they include real provider work. The service stress-test timings remain a separate measurement boundary. Earlier failures remain in the evidence: - The original five-minute Daytona allocation timeout never reached model execution. After normal owned-stack restore, its durable cleanup record was `expired` / `success`. The cause of that original allocation timeout remains unknown; a later success establishes recovery only. - Initial continuation setup used unsupported generic agent-update fields and returned HTTP 409 before dispatch. Setup was corrected to use the supported skill-assignment and versioned instruction commands. - The intervening completed native turn read repository bytes and ran the probe, but omitted the verifier JSON under the older test agent's overly-specific instruction file. Its strict receipt validator failed; it is not counted as a qualifying turn. Correcting the test agent's instruction file and sending an explicit task-scoped wake produced the qualifying follow-up above. - The pinned application's immutable rate card omits `gpt-5.4-mini`, so completed usage triggered the normal block-on-unpriced budget policy. Supported append-only accounting corrections estimated the three completed runs using the [official OpenAI model rate card](https://developers.openai.com/api/docs/models/gpt-5.4-mini): $0.75 input, $0.075 cached input, $4.50 output per million tokens, assuming standard processing. Estimates totaled 12.482655 cents. Original usage and missing-price records are preserved; the $1 hard stop and unpriced-usage guard stayed active. - Model shell attempts included a missing `xxd` command and incorrect guessed file paths. Those failed calls and subsequent successful actual verifier calls remain visible in complete event streams. No zero-tool-error claim is made. No product source changed during this continuation. The previously measured contention, cold-start and memory limits remain. The later merge resolution is covered by the separate integration checks above; these hosted receipts qualify their recorded candidate. ### Hosted stress test — October 29, 2026 **Hosted acceptance:** full native-agent execution and a changed-skill follow-up pass on the recorded hosted candidate. The final integration section above records the subsequent conflict resolution and its separate checks. Tested baseline `929e840595c8933ca485ac7a2e99413e1e11ca64` and this exact candidate sequentially on one disposable TEST tenant, with external Neon PostgreSQL and actual S3. The fixture contained **1,360 files / 22.4 MB / ten skills sharing one repository**. Measurements cover deployed skill-preparation and native-context services in an adjacent diagnostic process, not a complete agent turn. The container had **24 vCPU / 24 GB**. | Warm workload | Median before → after | p95 before → after | DB returned value bytes/preparation before → after | |---|---:|---:|---:| | One skill, serial | 1,060 → 125 ms | 1,303 → 155 ms | 22,610,389 → 1,771 | | One skill, four concurrent | 4,415 → 297 ms | 5,143 → 328 ms | 22,610,389 → 1,771 | | Ten skills, serial | 5,723 → 535 ms | 6,057 → 600 ms | 224,739,030 → 10,671 | | Ten skills, four concurrent | 24,410 → 1,986 ms | 24,833 → 2,221 ms | 224,739,030 → 10,671 | - Candidate warm preparation performed **zero S3 GETs**. Ordinary-pool queries fell from 16 to 9 for one skill and 61 to 9 for ten, excluding dedicated lock connections. DB numbers measure returned values before Drizzle decoding, not wire bytes. Baseline/candidate sample counts were 30/100, 32/100, 5/50 and 8/48 respectively; the small baseline ten-skill samples are comparative evidence, not SLO estimates. - **Application-UID soak:** 800 ten-skill preparations over 10.3 minutes, four workers paced by 2.5 seconds; **zero failures**, median **559 ms**, p95 **775 ms**, p99 **910 ms**, zero warm S3 reads. All 726 accompanying health/company-list requests returned HTTP 200. Their end-to-end p95 was 569/502 ms, including network latency. The probe overlaps most of the soak. Soak DB-response capture was limited to its first 60 seconds. - **Important remaining costs:** an unpaced 16-way ten-skill burst had p95 **8.32 seconds** because company-level preparation serializes. Cold preparation took approximately **1.1–2.5 seconds** for one skill and **7.4–10.0 seconds** for ten. Ten-skill diagnostic RSS remained about **1.17 GiB** (baseline 1.18 GiB), and the soak peaked at **1.35 GiB**. A concurrent whole-container sample was 3.45 GB. This does not establish suitability for a small-memory host or eliminate per-entrypoint native asset duplication. - **Upgrade without a manual data migration passed:** legacy snapshot JSON shrank from 22,465,691 bytes to `[]`, with a stored package and zero pending conversions. - **Recovery passed:** sixteen concurrent cold requests coalesced into two S3 GETs; full bytes/binary/executable modes matched; same-size corruption repaired; an injected storage failure preserved warm access and failed cold access safely. A disabled public-Git source denied recovery, and after the actual five-minute backoff its exact SHA reconstructed all 229 files. Cross-company descriptor access was denied. Private-Git credential revocation was not tested. - **Retention passed:** reclaimed 27,754,496 allocated cache bytes, deleted an unreferenced package row and both objects, preserved aged authored history, and expired/reacquired reconstructible Git content. A version pinned by the failed native run was correctly retained. Only owned fixture timestamps were aged. - **Browser UI passed:** authored skill creation, saved edit surviving reload, version history, and restoration of earlier content. - **Initial native attempt (superseded by the qualifying turns above):** one real run failed at Daytona allocation after five minutes (`setup_failed`), before any model execution. Provider cleanup also reported failure. That attempt does not count as a passing native turn. Its receipt and all evidence remain preserved; its cleanup later recorded success after normal restoration. - Initial A/B commands ran as SSH root. Diagnostic-owned lock/cache permissions caused one setup HTTP 500 and the first UID-1000 soak to fail; exact fixture paths were repaired. The final soak, retention and recovery ran as application UID 1000. A fresh UID-1000 one-skill batch also passed (30 samples, median 116 ms, p95 321 ms, 1,771 DB value bytes/preparation). Earlier harness-export, SSH, npm provenance, backoff and UI-wait failures remain recorded alongside their successful retries. - Private evidence includes raw timings, assertions, HTTP probes, screenshots and failure/cleanup receipts. Initial failed-campaign cleanup suspended and retained the owned TEST tenant and released the shared QA account lease at **15:22:41 UTC**. The tenant was subsequently resumed under its existing ownership for the native execution qualification above. Final cleanup completed at **15:53:09 UTC**: the account lease is released and the tenant is suspended/retained under the original October 30, 12:24:52 UTC retention deadline. Its separate stack lease remains held; no active or pending-cleanup environment lease remained. The original retention window is deliberately preserved even after successful continuation. - Earlier hosted-tested head: `a2e597d800eb989d565780e7aa947d5368676444`, integrated with master `929e840595`. The earlier merge conflicts were resolved at this head. [Current-head CI](https://github.com/paperclipai/paperclip/actions/runs/40884087629) passed; all checks are complete with 55 successes, two neutral reports, two skips, and no failures. [Apex review 15](https://github.com/paperclipai/paperclip/pull/18082#issuecomment-6480257258) passed 5/5 with zero findings on this exact head. All review conversations are resolved. - Ten real-filesystem boundary cases and server typecheck pass locally for the security fix. Coverage includes cache roots, descendants, individual files, symlink aliases, recursive ancestors, a future concurrent cache fill, and allowed sibling directories. [Current-head private-project integration tests](https://github.com/paperclipai/paperclip/actions/runs/40884087629/job/123483306405) passed all 29 cases, including authorized and unauthorized imports of a cached private package. Full typecheck, build, server suites, all eight browser shards, and Runner checks passed in current-head CI. Local database tests could not run because PostgreSQL could not initialize; this limitation is recorded below. - The earlier generated migration preserved the newest five snapshots. The final integration renumbers its unchanged SQL to 0415. Migration safety/numbering checks pass. Its SQL is byte-for-byte identical to the previously verified idempotent skill migration; repeated application on this latest schema was blocked by the same local database startup failure. - The broader verification before the final migration-only rebase passed 1,025 package, lifecycle, remote-launch, native-session, and asset-retention tests, 52 focused UI tests, full workspace typecheck/build, token gates, and map checks. The linked complete CI run passed before the latest focused fixes. - A disposable MinIO instance passed multipart upload, verified read-back, and cold restoration of an 18 MB archive. - Twenty warm samples with a synthetic 1,349-file, 22.8 MB repository retained five metadata queries and zero object reads. Median preparation was 256 ms for one selected skill and 691 ms for ten, with 5 ms emulated network delay each way. These are local measurements, not production latency guarantees. - No production instance was changed. Earlier verification failures and their disposition are retained below. <details> <summary>Earlier failures, review findings, fixes, and rerun evidence</summary> - The first CI pass found a stale inventory-span expectation and a missing repository-read span. Both are fixed; all three observability tests pass. One browser test copied page text into its YAML parser after reload; its first unchanged-head retry passed, but the race recurred after rebasing. The test now waits for the renamed URL and completed reload before copying the editor, retaining its original assertions. The earlier full local suite did not complete cleanly: it reported setup timeouts and assertions, while isolated relevant reruns passed. The complete current-head CI run closes that broad verification gap. No production instance was changed. - The first Apex review scored 2/5 and identified six issues. The fixes protect authored history even when it shares an in-flight Git upload, recheck upload expiry during orphan deletion, bound failed-upload cleanup, retain per-version kind/encoding metadata, add sanitized failure diagnostics, and correct the migration guide. The final focused run passes all 140 tests; the preceding eight-file run passed all 149 tests, including local storage and S3 diagnostics. Server typecheck and migration safety/numbering checks pass after the fixes. The second Apex review scored 1/5 and found unbounded maintenance storage calls and mismatched package/Git batch limits. Those are fixed with a 30-second cancellable cleanup deadline, shared 100 MiB/10,000-file scanner and storage limits, and bounded Git read batches. The proposed manual lockfile edit was rejected with evidence of the enforced CI-owned lockfile policy. All 19 storage/recovery unit tests and server typechecking pass. The new database-backed cleanup/conversion tests were locally skipped because the host exhausted its PostgreSQL semaphore capacity (confirmed directly by initdb). That gap is closed by current-head CI: [package-store tests](https://github.com/paperclipai/paperclip/actions/runs/40771320775/job/123109300889) pass all 18 cases and [package-worker tests](https://github.com/paperclipai/paperclip/actions/runs/40771320775/job/123109301157) pass all 7, with no skips in either suite. The corrected YAML browser shard passes. A separate planning-fixture test failed its cleanup DELETE with an activity-log foreign key violation after its behavior assertions passed; its one unchanged-head retry passed. The third Apex review scored 1/5 and identified a one-slot pool deadlock, projected path limits, cleanup holding the preparation lock during archive reads, and a publication/expiry race. These are fixed with transaction-local reads, prefix-aware bounds, isolated verification, and shared package row locks with a publication grace. The separate Paperclip review also found stale historical inspection, eager history downloads, and conversion retries blocking sleep. Those are fixed. Local PostgreSQL capacity recovered: the new database regressions ran, including the one-slot fork, paused storage during a warm turn, and a locked publication during expiry. The expanded run passed 144/145 tests; its remaining assertion still expected file bodies from the version list and was updated to fetch the selected version. The corrected company-skill suite passes all 81 tests, and the final package/projection run passes all 27. All 52 focused UI tests pass after updating their query-provider fixtures; the first UI run exposed a fixture remount, and the follow-up exposed an editing syntax error, both corrected. Full workspace typecheck and build, token gates, and map checks pass. The sandbox initially blocked the build tool’s local IPC socket; the authorized build rerun passed. Master then claimed migration 0401. The branch is rebased on |