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Author	SHA1	Message	Date
Nicky LeachandPaperclip	9f4a956b90	Add durable agent runtime synchronization hooks (#16499 ) ## Thinking Path > - Paperclip manages agents and their runtime configuration. > - Plugins can maintain external agent computers. > - Configuration and file saves currently miss durable plugin delivery. > - A transient activity notification cannot recover after interruption. > - This pull request adds an opt-in agent runtime resource stream. > - The existing dispatcher delivers and acknowledges its committed work. > - Plugins can prepare computers when configuration changes. ## Linked Issues or Issue Description Related: #15631 and #16203 establish agent lifecycle and native durable delivery. Problem Plugins cannot reliably react to agent configuration and instruction changes without polling or waiting for execution. Proposed solution Add an opt-in `agent_runtime` stream to the existing resource journal. Record changes at the database mutation and managed file audit boundaries. Wake the dispatcher with content-free commit notifications. Provide scoped runtime inputs to the selected lifecycle plugin. Alternatives considered Route-only activity events miss service and background writers. Scheduled scans delay changes and repeatedly query unchanged state. Roadmap alignment This extends the existing plugin and agent configuration work. ## What Changed - Add durable update/delete events for agent runtime state, including an existing-agent baseline. - Capture configuration changes, instruction edits, deletion, restore, and managed run writeback. - Add commit notifications and a reconnect scan. Register one listener for configured, enabled runtime subscribers. Release it when none remain. - Keep HTTP startup independent of queued plugin callbacks. - Add `ctx.agents.getRuntime`. Require lifecycle capability, invocation company, enabled plugin, and owning lifecycle selection. - Keep legacy agent/project subscriptions isolated. Manual inbox reads retain both legacy streams. - Resolve recovered instruction paths without reading or hashing bundle contents. Use the company reporting graph for runtime health. - Repair missed file events on identical save/deletion retries after a journal failure; preserve content tokens and conditional-write checks. - Correlate file audits with runtime revisions to deduplicate recorded retries without a new table. Bound the lookup with the existing company/timestamp index. - Document the contract, migration, access boundaries, and session-connection requirement. ## Verification - Rebased the full stack onto origin/master after #16507. - Final replayed stack: `pnpm -r typecheck` and `pnpm build` passed. - All 132 affected runtime, skill, connector, publication, instruction, managed-agent, and delivery tests passed after the latest-master rebase. Workspace typecheck and build passed. - Journal failure injection verifies recovery on identical file writes, deletions, and instruction retries from an acknowledged inbox. - Deduplication follow-up: 80 runtime/instruction/delivery tests and server typecheck passed. Repeated retries create no audit/events; old hashes returning after an intervening commit still repair delivery. Built-in/native instruction writer regressions passed all 56 tests. - PR 1 follow-up tests cover valid/cyclic reporting chains, listener registration failure, multiple subscribers, global/company disable, re-enable, unload, and startup with blocked callbacks. - Database coverage includes rollback, journal failure, no-op suppression, file saves/deletion, ordering/replay, owner/company denial, independent-client commits, and real listener loss/reconnect. - SDK/shared suites passed 1,059 tests during implementation. CLI/delivery regressions also passed. - Migration safety, map checks, diff whitespace, and local secrets/PII scan passed. - Hosted CI and security checks are fully green at `b296405e2`. Standard Greptile and Apex both returned 5/5 with no unresolved findings. - The broad local suite encountered an unchanged diagnostic test that rejects the word "private" from an error stack. This worktree lives under /private/tmp. The same unchanged diagnostic suite passed all 108 tests in the original checkout. Hosted full-suite checks provide exact-head verification. ## Risks - Apply migration 0347 before enabling a runtime subscriber. Runtime notifications require session-level PostgreSQL LISTEN. Transaction-mode poolers are unsupported for this opt-in feature. - Database triggers share the mutation transaction. Journal failure prevents configuration commits. Trigger work adds a journal insert to relevant changes. - Filesystem publication and SQL commit are separate boundaries. Direct filesystem edits do not emit hooks. External clients must fence stale revisions and retain conditional-write checks. - The reader returns only that plugin's own instance secrets. Keep them out of UI data, logs, plugin state, and agent files. - No private transport integration or live remote computer qualification is included. ## Model Used OpenAI Codex, GPT-6, with reasoning, repository inspection, code execution, and testing. The exact deployment 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 references) - [x] My branch name describes the change and contains no internal Paperclip ticket id - [x] I have run tests locally and they pass (focused suites; broad local limitation documented 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>	2026-10-16 07:53:04 -07:00
Nicky LeachandPaperclip	2dd9811e8b	Own agent hiring and termination in a lifecycle module (#15631 ) ## Thinking Path > - Paperclip manages AI agents and their work. > - Agent creation, approval, pause, and termination change whether an agent can work. > - These changes currently use separate service and database paths. > - Some agents need setup after their record exists and before their harness can run. > - This PR adds one module that owns those state changes and their transactions. > - The module records progress and retries incomplete work after a server restart. ## Linked Issues or Issue Description Problem or motivation A hire can become active before its execution environment is ready. Direct agent state writes also bypass one common lifecycle boundary. Termination does not have a durable step for resource cleanup. Proposed solution Use agent lifecycle commands for hiring, approval, pause, resume, and termination. Keep proposed hires pending until approval. Prepare each approved hire, test its saved harness configuration, and then permit work. Wait for required plugin work before completing a step. Alternatives considered A general database commit hook would expose transaction details to callers. A timer alone would delay each new hire. This module owns each command transaction and starts its worker after commit. A periodic scan recovers work after a process stops. Roadmap alignment This change adds the lifecycle boundary for the existing agent and plugin systems. It does not add a user interface or a provider implementation. It replaces the lifecycle delivery approach in #15391. Related proposals include #11475 and #13099; this change does not add their external executor protocols. ## What Changed - Add durable approval, preparation, verification, pause, resume, stop, and cleanup states. - Keep agent creation, lifecycle state, configuration writes, and agent record deletion behind `modules/agent-lifecycle`. Keep validation, credential rules, reads, onboarding, invitations, general approvals, and company data deletion in their services. - Commit a hire before the remaining onboarding or invitation work. Serialize requests with the existing dedicated database connection helper. Reuse the hire after a failed attempt. - Keep accepted work in the run queue during setup. Require execution and cleanup evidence before completing pause or termination. - Retain the original credential owner when approving migrated hires. - Start lifecycle work after each command commits. Use database leases and revision checks for retries and late results. - Add a generic required plugin method and capability. Store the required plugin IDs for each agent. Track host and plugin completion separately. - Keep harness verification and credential rules in services. Supply their results to lifecycle through explicit ports. Reject failed logins and incomplete probes. - Remove reverse imports from lifecycle adapters into services. Share record queries and validation below both layers. - Use one hire decision path for agent IDs and approval IDs. Resolve the approval and agent change in one transaction. Expose policy reconciliation on the command object. - Save configuration and verification invalidation through one module operation. Ordinary commands own their transaction. Restrict the shared transaction integration to its listed callers. Reject identity, company, accounting, timestamp, and unknown fields. - Require completed termination before deleting agent records. The company deletion service calls the module through a separate deletion interface. - Save an approved secret before applying its agent binding. A failed binding leaves the secret approved. A retry reuses it. - Remove old permission and metadata export files. Move hire configuration rules out of lifecycle persistence. - Report failed worker steps and scans with operation context and known error codes. Omit provider messages, stacks, and configuration values. Document ordinary application use and extension rules. - Recover expired native owners only after execution stops. Retry cleanup of failed retained leases. Wait for setup in the live smoke script. - Keep manual, budget, and company pause reasons separate. Guard execution status writes with the ready state. - Add a migration, boundary checks, regression tests, and a lifecycle guide. Keep the current UI. - Limit periodic policy checks to 100 eligible agents per minute. Continue from the last agent ID. Exclude pending hires and agents in termination or a final state. Keep explicit company and budget updates immediate. ## Verification - Latest head `ccc3c86b0` aligns the shared status update schema with the PATCH route. All 15 shared tests, 104 server route/OpenAPI tests, 2 CLI tests, and shared/server/CLI TypeScript checks pass. The Greptile comment is fixed. CI is running; no new Apex review was requested for this small fix. - Rebase `75708ac94` rebases onto master at `2eb5187e4`. The backup test uses the shared 90-second timeout from master; the older timeout commit was removed. The affected backup test passes. - Agent budget edits now pass the target agent ID through enforcement. All 50 affected tests, server TypeScript, and 11 boundary tests pass. Both configuration update paths have regression coverage. CI is running on the latest head. No new Apex review was requested for these small fixes. - Rebase `9b568666a` preserves the run-control extraction and delivery-work startup changes from master. All 559 affected tests, server TypeScript, and 11 boundary tests pass. CI and Apex review are running on the final head. - The policy scan fix passes 56 lifecycle and diagnostic tests, 24 policy and caller tests, and 11 boundary tests. A regression test checks the page limit, interval, excluded states, and cursor wraparound. - Rebase `fd4698750` passes all 611 tests in eight affected lifecycle, route, and heartbeat suites. Server TypeScript and all 11 module boundary tests pass. The company deletion rollback and concurrent hire tests are included. - Follow-up `00aac7646` fixes the failed decision deletion test and the public update schema. All 126 affected server tests, 8 shared tests, 2 CLI tests, and 11 boundary tests pass. Shared, server, CLI, and UI TypeScript checks pass. - Server TypeScript passes: `pnpm --filter @paperclipai/server exec tsc --noEmit`. - All 11 boundary tests pass: `node --test scripts/check-module-boundaries.test.mjs`. The repository boundary scan also passes. - All 68 lifecycle, failure diagnostic, and harness verification tests pass. Tests reject forbidden fields through the root command, combined transition command, and restricted transaction integration. They also check invalid fields returned by configuration preparation. - Failure tests cover host work, plugin work, claims, renewals, deferrals, and scans. Log tests check known error codes and exclusion of private error contents. - All 355 tests in 10 existing caller suites pass. These tests cover secret approval, pairing, pending hires, credentials, company import, built-in agents, managed agents, instructions, and skills. - The branch is rebased onto `origin/master` at `2eb5187e4`. The queue guards and cancellation lock fix use the extracted heartbeat queue. Agent cancellation uses the extracted run-control file. The source diff scan found no secrets or private URLs. - Earlier checks cover approval retries, rollback, late verification results, policy holds, deletion rollback, concurrent company deletion, and queue admission during setup. - Before the rebase, CI passed on `00aac7646` and Greptile Apex rated it 5/5 with no open comments. CI and a new Apex review are pending for the rebased commit. The branch has no merge conflicts. - The full local build and native Dot suite were not run. The host has no Cargo. No live provider test was run. ## Risks - Background policy recovery takes more than one minute when more than 100 agents are eligible. Explicit company and budget updates still reconcile immediately. - The restricted configuration integration keeps an agent reference and its dependent records in one transaction. It cannot change a budget or invoke a lifecycle transition. A periodic scan starts pending setup after that transaction commits. - Secret approval and binding use separate transactions. A failed binding can leave an approved secret with no agent binding. - New approved hires remain unavailable until setup and verification complete. Existing clients see `paused` during these steps. This PR does not change the UI. - Migration `0320_daily_onslaught.sql` maps existing statuses and pause reasons. It does not create external resources or claim that an existing harness passed verification. - Use a coordinated server update for this migration. Older server versions can write legacy status without the new lifecycle checks. - A failed onboarding or invitation request can leave a committed hire. A retry reuses that hire and completes the remaining records. - Deletion requires completed termination. Company deletion can require another request while cleanup is pending. - Required plugins must make repeated calls safe and reject older revisions. A disabled or removed required plugin blocks completion until it is restored. - A new hire can run a second harness test after the existing UI test. Some adapters can charge for this test. - No live provider test was run. Provider implementation and resource backfill remain separate work. ## Model Used OpenAI GPT-6 through Codex, with reasoning, code tools, and local 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 described the issue in this PR with the feature request field labels - [x] I have not referenced internal or instance-local issues or links - [x] My branch name describes the change - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation - [x] I have considered and documented risks - [x] Targeted local tests pass - [x] All Paperclip CI gates are green on the new commit - [x] Greptile Apex is 5/5 with no open comments on the new commit - [x] I will address review comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing>	2026-10-09 09:05:12 -07:00
DottaandFry	3ca196b0a6	feat(agents): persist agent files across tasks without revision history (#14420 ) ## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - An agent needs personal files across tasks and sessions. > - AGENTS.md is one file in that directory. Supporting files need the same persistence. > - The Instructions Editor and agent runs must share one current directory. > - Concurrent runs should apply only the files they change. The last sync of the same file wins. > - This pull request uses existing file transport and removes temporary copies after sync. > - Old instruction-only sessions keep their restore contract. New saves do not create revision history. ## Linked Issues or Issue Description Refs #14325. This replaces its revision-oriented design with persistent agent files. Keep #14325 unmerged. Transport prerequisite #14416 merged first at `d172197117a14b80a1eb2d2835a0e7cce2679656`. This PR now targets master and remains below 100 changed files. Related work: #4513 and #8798 cover instruction tooling. This change handles run synchronization, cross-task personal files, browser editing, and old-session restoration. ## What Changed - Keep one current directory per company and agent. Point AGENT_HOME at a temporary working copy for each active run. Keep task files and provider HOME separate. - Restore text, binary files, and nested folders through workspace transport. Exclude remote agent files from task Git snapshots with a self-ignoring file inside the reserved runtime directory; never write through repository-controlled Git metadata. - Collect after the provider and child processes have stopped. Keep resumable conversation state. - Apply changed and deleted files under the agent lock. The last sync wins for the same file. Unrelated concurrent changes survive. - Remove temporary copies after successful sync, rejected sync, and staging failure. Register ownership before copying so restart recovery can remove interrupted preparation. Retry transient synchronization up to three times. Preserve the original remote lease reference until deletion succeeds; restart cleanup never acquires a replacement sandbox. Do not create captured directories or a conflict-review queue for new runs. - Keep browser editing, stale-draft protection, and streaming binary downloads. Keep the instruction entry and text editor limited to 1 MiB. - Keep historical agent-folder sync failures on their affected runs instead of repeating them above current saved instructions. Preserve legacy candidate review and current browser-save errors. Avoid duplicate quota warnings while retaining separate sync failures when they describe a different problem. - Require target-scoped caller grants for peer instruction access, while preserving self edits, responsible-user checks, and protected-change consent. - Treat full storage as a nonblocking run warning, never an agent pause or run-admission failure. Restore already-over-quota saved folders so ordinary agent cleanup can recover; warn on each run until cleanup. The run detail view shows the warning. - Allow 256 MiB per file, 2 GiB per directory, and 100,000 entries. Hash large files as streams. Check editor-save quotas with metadata instead of hashing unrelated files. - Preserve old native inputs, instruction-only copies, paths, digests, and pending legacy candidates. Adopt old revision heads once. New writes do not append history rows. - Add idempotent migration 0287 and verify upgrades from the preview tables and receipts. - Add nine interactive stories under Agents / Persistent files, including automatic incoming edits, stale browser drafts, and storage-limit diagnostics. ## Verification - Merge candidate: `4f5390107ec6ffd80a76d1d2e85530e66f21d079`, after merging current master and the landed transport prerequisite. Integration required no manual conflict resolution; the feature remains 99 changed files. Full workspace typecheck, production build, token gates, and 715 focused tests passed on this merge candidate. Fresh Greptile review is 5/5 with no unresolved findings. All 55 checks passed, with four conditional skips, including the build, typecheck, browser E2E, and canary dry run. A single retry recovered four jobs interrupted by runner shutdowns; no source changes were required. - Historical-warning UI fix: all 6,834 UI tests across 640 files passed, including regression coverage for three old failures, legacy preserved edits, and warnings scoped to the affected run. Full workspace typecheck, production build, Storybook build, and token gates passed. Browser-verified Storybook playtests passed for Historical Failures After Successful Save, Storage Limit, and Full Storage Run Warning. - Review follow-ups at `4e20c9fb2`: all 18 focused tests passed, including external Git directories, linked worktrees, symlinks, hardlinks, and distinct I/O failures alongside storage warnings. Server and UI typechecks, token gates, and the production build passed. - Storage warning regressions at `0724f3012`: all 33 directory tests and all five heartbeat-list tests passed, with no skips in their successful runs. They cover repeated runs while full, an already-over-quota saved folder, cleanup, warnings retained after unrelated save failures, and bounded warnings in large result JSON. Server typecheck passed after the final warning fixes. - Full workspace typecheck, production build, and token gates passed during this follow-up. Product E2E harness: 631 tests passed across 52 files; harness typecheck passed. Earlier native session/context and directory/legacy collection suites passed 537 tests; Runner unit/transport suites passed 329 tests. - Real E2E at `0724f3012` (before this follow-up): legacy local Codex and native Daytona Codex each passed six tasks, one server restart, seven independent assertions, and cleanup verification. Both prove browser-to-agent edits, agent-to-browser edits, nested/binary restoration, per-file last-sync-wins, a successful run after an oversized save rejection, and cleanup clearing the warning. - Native local Codex also passed the six-task quota flow before the final warning-retention fixes. That pass began at `918d1ed02` while the bounded-result warning fix was being edited, so it is not claimed as exact-final-head evidence. Its final-head rerun failed during embedded PostgreSQL bootstrap before any provider run: the macOS host had 87,365 of 87,381 SysV semaphores occupied. No unrelated services or kernel limits were changed. - The final-source report intentionally records 2/3 cells passed, preserving the blocked native-local attempt: `tests/runner-e2e/results/agent-files-quota-final-20260928-report/`. Earlier failed attempts and provenance notes remain under `tests/runner-e2e/results/agent-files-quota-final-20260928-input/` and the original campaign directories. - Daytona used immutable image `ghcr.io/paperclipai/paperclip-daytona-runner@sha256:5643f0d801417cae3581833a1a3bc6715b325e028602738d2652c44cac5dc6bf` and its exact Linux runner binary. Controller source is `0724f3012`; image source is recorded separately. - Legacy-session compatibility and all three ACP Stop/resume browser regressions passed on the prior validated feature head `169fab46d5af21caa2269b4c1b29b69c933a6951`. They assert the same provider session is retained and interrupted writes are not replayed. Migration upgrade tests also passed earlier. - Nine interactive stories are under Agents / Persistent files, including Full Storage Run Warning. Its playtest and visual browser inspection passed; the warning states that runs continue and the editor remains available. - Prior-head checks on `4e20c9fb2`: 55 passed, two conditional jobs skipped, no failures or pending checks. All eight browser E2E shards and their aggregate passed. Fresh Greptile review is 5/5 with no findings; all review threads are resolved, the security scan passed, and GitHub reports no merge conflicts. - The broad local follow-up test run was interrupted after host semaphore exhaustion affected isolated PostgreSQL instances. It also encountered the existing macOS long-path fixture failure and two timeout failures. This is not a claim that the full local suite passed. Logs are retained; focused storage/warning tests passed. ## Risks - A later sync can overwrite an earlier edit to the same file, including a saved browser edit. There is no text merge or retained version. This is the intended last-sync-wins policy. - A save that exceeds a storage limit is rejected and its temporary copy is discarded. The run itself continues normally, and later runs restore the last saved files with a warning until cleanup. Transient sync failures get bounded retries. An I/O failure partway through a sync can leave some files updated; a failed receipt does not claim whole-folder success. - Larger folders increase copy time, network traffic, and temporary disk usage. Active runs still need working copies. Terminal runs do not accumulate archives. Operators must provision disk for agents and configured concurrency; these limits are not company-wide quotas. - A restored old native session remains instruction-only until a fresh session starts. Its original conflict fence and existing pending candidates remain compatible. - Provider processes close at the collection boundary. Conversation resume remains available, but warm process reuse is lost. - Backups must include the instance filesystem and database. External bundles keep their existing behavior until explicitly moved to managed storage. ## Model Used OpenAI Codex, GPT-6 family. The session does not expose a more specific model ID or context-window size. Reasoning, code execution, and browser tools assisted this change. Real provider E2E uses `gpt-5.6-sol`. ## 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: Fry (Paperclip) <noreply@paperclip.ing>	2026-09-29 08:25:56 -05:00

Author

SHA1

Message

Date

Nicky LeachandPaperclip

9f4a956b90

Add durable agent runtime synchronization hooks (#16499 )

## Thinking Path

> - Paperclip manages agents and their runtime configuration.
> - Plugins can maintain external agent computers.
> - Configuration and file saves currently miss durable plugin delivery.
> - A transient activity notification cannot recover after interruption.
> - This pull request adds an opt-in agent runtime resource stream.
> - The existing dispatcher delivers and acknowledges its committed
work.
> - Plugins can prepare computers when configuration changes.

## Linked Issues or Issue Description

Related: #15631 and #16203 establish agent lifecycle and native durable
delivery.

**Problem**

Plugins cannot reliably react to agent configuration and instruction
changes without polling or waiting for execution.

**Proposed solution**

Add an opt-in `agent_runtime` stream to the existing resource journal.
Record changes at the database mutation and managed file audit
boundaries. Wake the dispatcher with content-free commit notifications.
Provide scoped runtime inputs to the selected lifecycle plugin.

**Alternatives considered**

Route-only activity events miss service and background writers.
Scheduled scans delay changes and repeatedly query unchanged state.

**Roadmap alignment**

This extends the existing plugin and agent configuration work.

## What Changed

- Add durable update/delete events for agent runtime state, including an
existing-agent baseline.
- Capture configuration changes, instruction edits, deletion, restore,
and managed run writeback.
- Add commit notifications and a reconnect scan. Register one listener
for configured, enabled runtime subscribers. Release it when none
remain.
- Keep HTTP startup independent of queued plugin callbacks.
- Add `ctx.agents.getRuntime`. Require lifecycle capability, invocation
company, enabled plugin, and owning lifecycle selection.
- Keep legacy agent/project subscriptions isolated. Manual inbox reads
retain both legacy streams.
- Resolve recovered instruction paths without reading or hashing bundle
contents. Use the company reporting graph for runtime health.
- Repair missed file events on identical save/deletion retries after a
journal failure; preserve content tokens and conditional-write checks.
- Correlate file audits with runtime revisions to deduplicate recorded
retries without a new table. Bound the lookup with the existing
company/timestamp index.
- Document the contract, migration, access boundaries, and
session-connection requirement.

## Verification

- Rebased the full stack onto origin/master after #16507.
- Final replayed stack: `pnpm -r typecheck` and `pnpm build` passed.
- All 132 affected runtime, skill, connector, publication, instruction,
managed-agent, and delivery tests passed after the latest-master rebase.
Workspace typecheck and build passed.
- Journal failure injection verifies recovery on identical file writes,
deletions, and instruction retries from an acknowledged inbox.
- Deduplication follow-up: 80 runtime/instruction/delivery tests and
server typecheck passed. Repeated retries create no audit/events; old
hashes returning after an intervening commit still repair delivery.
Built-in/native instruction writer regressions passed all 56 tests.
- PR 1 follow-up tests cover valid/cyclic reporting chains, listener
registration failure, multiple subscribers, global/company disable,
re-enable, unload, and startup with blocked callbacks.
- Database coverage includes rollback, journal failure, no-op
suppression, file saves/deletion, ordering/replay, owner/company denial,
independent-client commits, and real listener loss/reconnect.
- SDK/shared suites passed 1,059 tests during implementation.
CLI/delivery regressions also passed.
- Migration safety, map checks, diff whitespace, and local secrets/PII
scan passed.
- Hosted CI and security checks are fully green at `b296405e2`. Standard
Greptile and Apex both returned 5/5 with no unresolved findings.
- The broad local suite encountered an unchanged diagnostic test that
rejects the word "private" from an error stack. This worktree lives
under /private/tmp. The same unchanged diagnostic suite passed all 108
tests in the original checkout. Hosted full-suite checks provide
exact-head verification.

## Risks

- Apply migration 0347 before enabling a runtime subscriber. Runtime
notifications require session-level PostgreSQL LISTEN. Transaction-mode
poolers are unsupported for this opt-in feature.
- Database triggers share the mutation transaction. Journal failure
prevents configuration commits. Trigger work adds a journal insert to
relevant changes.
- Filesystem publication and SQL commit are separate boundaries. Direct
filesystem edits do not emit hooks. External clients must fence stale
revisions and retain conditional-write checks.
- The reader returns only that plugin's own instance secrets. Keep them
out of UI data, logs, plugin state, and agent files.
- No private transport integration or live remote computer qualification
is included.

## Model Used

OpenAI Codex, GPT-6, with reasoning, repository inspection, code
execution, and testing. The exact deployment 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 references)
- [x] My branch name describes the change and contains no internal
Paperclip ticket id
- [x] I have run tests locally and they pass (focused suites; broad
local limitation documented 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>

2026-10-16 07:53:04 -07:00

Nicky LeachandPaperclip

2dd9811e8b

Own agent hiring and termination in a lifecycle module (#15631 )

## Thinking Path

> - Paperclip manages AI agents and their work.
> - Agent creation, approval, pause, and termination change whether an
agent can work.
> - These changes currently use separate service and database paths.
> - Some agents need setup after their record exists and before their
harness can run.
> - This PR adds one module that owns those state changes and their
transactions.
> - The module records progress and retries incomplete work after a
server restart.

## Linked Issues or Issue Description

**Problem or motivation**

A hire can become active before its execution environment is ready.
Direct agent state writes also bypass one common lifecycle boundary.
Termination does not have a durable step for resource cleanup.

**Proposed solution**

Use agent lifecycle commands for hiring, approval, pause, resume, and
termination. Keep proposed hires pending until approval. Prepare each
approved hire, test its saved harness configuration, and then permit
work. Wait for required plugin work before completing a step.

**Alternatives considered**

A general database commit hook would expose transaction details to
callers. A timer alone would delay each new hire. This module owns each
command transaction and starts its worker after commit. A periodic scan
recovers work after a process stops.

**Roadmap alignment**

This change adds the lifecycle boundary for the existing agent and
plugin systems. It does not add a user interface or a provider
implementation. It replaces the lifecycle delivery approach in #15391.
Related proposals include #11475 and #13099; this change does not add
their external executor protocols.

## What Changed

- Add durable approval, preparation, verification, pause, resume, stop,
and cleanup states.
- Keep agent creation, lifecycle state, configuration writes, and agent
record deletion behind `modules/agent-lifecycle`. Keep validation,
credential rules, reads, onboarding, invitations, general approvals, and
company data deletion in their services.
- Commit a hire before the remaining onboarding or invitation work.
Serialize requests with the existing dedicated database connection
helper. Reuse the hire after a failed attempt.
- Keep accepted work in the run queue during setup. Require execution
and cleanup evidence before completing pause or termination.
- Retain the original credential owner when approving migrated hires.
- Start lifecycle work after each command commits. Use database leases
and revision checks for retries and late results.
- Add a generic required plugin method and capability. Store the
required plugin IDs for each agent. Track host and plugin completion
separately.
- Keep harness verification and credential rules in services. Supply
their results to lifecycle through explicit ports. Reject failed logins
and incomplete probes.
- Remove reverse imports from lifecycle adapters into services. Share
record queries and validation below both layers.
- Use one hire decision path for agent IDs and approval IDs. Resolve the
approval and agent change in one transaction. Expose policy
reconciliation on the command object.
- Save configuration and verification invalidation through one module
operation. Ordinary commands own their transaction. Restrict the shared
transaction integration to its listed callers. Reject identity, company,
accounting, timestamp, and unknown fields.
- Require completed termination before deleting agent records. The
company deletion service calls the module through a separate deletion
interface.
- Save an approved secret before applying its agent binding. A failed
binding leaves the secret approved. A retry reuses it.
- Remove old permission and metadata export files. Move hire
configuration rules out of lifecycle persistence.
- Report failed worker steps and scans with operation context and known
error codes. Omit provider messages, stacks, and configuration values.
Document ordinary application use and extension rules.
- Recover expired native owners only after execution stops. Retry
cleanup of failed retained leases. Wait for setup in the live smoke
script.
- Keep manual, budget, and company pause reasons separate. Guard
execution status writes with the ready state.
- Add a migration, boundary checks, regression tests, and a lifecycle
guide. Keep the current UI.
- Limit periodic policy checks to 100 eligible agents per minute.
Continue from the last agent ID. Exclude pending hires and agents in
termination or a final state. Keep explicit company and budget updates
immediate.

## Verification

- Latest head `ccc3c86b0` aligns the shared status update schema with
the PATCH route. All 15 shared tests, 104 server route/OpenAPI tests, 2
CLI tests, and shared/server/CLI TypeScript checks pass. The Greptile
comment is fixed. CI is running; no new Apex review was requested for
this small fix.

- Rebase `75708ac94` rebases onto master at `2eb5187e4`. The backup test
uses the shared 90-second timeout from master; the older timeout commit
was removed. The affected backup test passes.
- Agent budget edits now pass the target agent ID through enforcement.
All 50 affected tests, server TypeScript, and 11 boundary tests pass.
Both configuration update paths have regression coverage. CI is running
on the latest head. No new Apex review was requested for these small
fixes.

- Rebase `9b568666a` preserves the run-control extraction and
delivery-work startup changes from master. All 559 affected tests,
server TypeScript, and 11 boundary tests pass. CI and Apex review are
running on the final head.
- The policy scan fix passes 56 lifecycle and diagnostic tests, 24
policy and caller tests, and 11 boundary tests. A regression test checks
the page limit, interval, excluded states, and cursor wraparound.

- Rebase `fd4698750` passes all 611 tests in eight affected lifecycle,
route, and heartbeat suites. Server TypeScript and all 11 module
boundary tests pass. The company deletion rollback and concurrent hire
tests are included.

- Follow-up `00aac7646` fixes the failed decision deletion test and the
public update schema. All 126 affected server tests, 8 shared tests, 2
CLI tests, and 11 boundary tests pass. Shared, server, CLI, and UI
TypeScript checks pass.

- Server TypeScript passes: `pnpm --filter @paperclipai/server exec tsc
--noEmit`.
- All 11 boundary tests pass: `node --test
scripts/check-module-boundaries.test.mjs`. The repository boundary scan
also passes.
- All 68 lifecycle, failure diagnostic, and harness verification tests
pass. Tests reject forbidden fields through the root command, combined
transition command, and restricted transaction integration. They also
check invalid fields returned by configuration preparation.
- Failure tests cover host work, plugin work, claims, renewals,
deferrals, and scans. Log tests check known error codes and exclusion of
private error contents.
- All 355 tests in 10 existing caller suites pass. These tests cover
secret approval, pairing, pending hires, credentials, company import,
built-in agents, managed agents, instructions, and skills.
- The branch is rebased onto `origin/master` at `2eb5187e4`. The queue
guards and cancellation lock fix use the extracted heartbeat queue.
Agent cancellation uses the extracted run-control file. The source diff
scan found no secrets or private URLs.
- Earlier checks cover approval retries, rollback, late verification
results, policy holds, deletion rollback, concurrent company deletion,
and queue admission during setup.
- Before the rebase, CI passed on `00aac7646` and Greptile Apex rated it
5/5 with no open comments. CI and a new Apex review are pending for the
rebased commit. The branch has no merge conflicts.
- The full local build and native Dot suite were not run. The host has
no Cargo. No live provider test was run.

## Risks

- Background policy recovery takes more than one minute when more than
100 agents are eligible. Explicit company and budget updates still
reconcile immediately.

- The restricted configuration integration keeps an agent reference and
its dependent records in one transaction. It cannot change a budget or
invoke a lifecycle transition. A periodic scan starts pending setup
after that transaction commits.
- Secret approval and binding use separate transactions. A failed
binding can leave an approved secret with no agent binding.
- New approved hires remain unavailable until setup and verification
complete. Existing clients see `paused` during these steps. This PR does
not change the UI.
- Migration `0320_daily_onslaught.sql` maps existing statuses and pause
reasons. It does not create external resources or claim that an existing
harness passed verification.
- Use a coordinated server update for this migration. Older server
versions can write legacy status without the new lifecycle checks.
- A failed onboarding or invitation request can leave a committed hire.
A retry reuses that hire and completes the remaining records.
- Deletion requires completed termination. Company deletion can require
another request while cleanup is pending.
- Required plugins must make repeated calls safe and reject older
revisions. A disabled or removed required plugin blocks completion until
it is restored.
- A new hire can run a second harness test after the existing UI test.
Some adapters can charge for this test.
- No live provider test was run. Provider implementation and resource
backfill remain separate work.

## Model Used

OpenAI GPT-6 through Codex, with reasoning, code tools, and local 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 described the issue in this PR with the feature request
field labels
- [x] I have not referenced internal or instance-local issues or links
- [x] My branch name describes the change
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation
- [x] I have considered and documented risks
- [x] Targeted local tests pass
- [x] All Paperclip CI gates are green on the new commit
- [x] Greptile Apex is 5/5 with no open comments on the new commit
- [x] I will address review comments before requesting merge

---------

Co-authored-by: Paperclip <noreply@paperclip.ing>

2026-10-09 09:05:12 -07:00

DottaandFry

3ca196b0a6

feat(agents): persist agent files across tasks without revision history (#14420 )

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - An agent needs personal files across tasks and sessions.
> - AGENTS.md is one file in that directory. Supporting files need the
same persistence.
> - The Instructions Editor and agent runs must share one current
directory.
> - Concurrent runs should apply only the files they change. The last
sync of the same file wins.
> - This pull request uses existing file transport and removes temporary
copies after sync.
> - Old instruction-only sessions keep their restore contract. New saves
do not create revision history.

## Linked Issues or Issue Description

Refs #14325. This replaces its revision-oriented design with persistent
agent files. Keep #14325 unmerged.

Transport prerequisite #14416 merged first at
`d172197117a14b80a1eb2d2835a0e7cce2679656`. This PR now targets master
and remains below 100 changed files.

Related work: #4513 and #8798 cover instruction tooling. This change
handles run synchronization, cross-task personal files, browser editing,
and old-session restoration.

## What Changed

- Keep one current directory per company and agent. Point AGENT_HOME at
a temporary working copy for each active run. Keep task files and
provider HOME separate.
- Restore text, binary files, and nested folders through workspace
transport. Exclude remote agent files from task Git snapshots with a
self-ignoring file inside the reserved runtime directory; never write
through repository-controlled Git metadata.
- Collect after the provider and child processes have stopped. Keep
resumable conversation state.
- Apply changed and deleted files under the agent lock. The last sync
wins for the same file. Unrelated concurrent changes survive.
- Remove temporary copies after successful sync, rejected sync, and
staging failure. Register ownership before copying so restart recovery
can remove interrupted preparation. Retry transient synchronization up
to three times. Preserve the original remote lease reference until
deletion succeeds; restart cleanup never acquires a replacement sandbox.
Do not create captured directories or a conflict-review queue for new
runs.
- Keep browser editing, stale-draft protection, and streaming binary
downloads. Keep the instruction entry and text editor limited to 1 MiB.
- Keep historical agent-folder sync failures on their affected runs
instead of repeating them above current saved instructions. Preserve
legacy candidate review and current browser-save errors. Avoid duplicate
quota warnings while retaining separate sync failures when they describe
a different problem.
- Require target-scoped caller grants for peer instruction access, while
preserving self edits, responsible-user checks, and protected-change
consent.
- Treat full storage as a nonblocking run warning, never an agent pause
or run-admission failure. Restore already-over-quota saved folders so
ordinary agent cleanup can recover; warn on each run until cleanup. The
run detail view shows the warning.
- Allow 256 MiB per file, 2 GiB per directory, and 100,000 entries. Hash
large files as streams. Check editor-save quotas with metadata instead
of hashing unrelated files.
- Preserve old native inputs, instruction-only copies, paths, digests,
and pending legacy candidates. Adopt old revision heads once. New writes
do not append history rows.
- Add idempotent migration 0287 and verify upgrades from the preview
tables and receipts.
- Add nine interactive stories under **Agents / Persistent files**,
including automatic incoming edits, stale browser drafts, and
storage-limit diagnostics.

## Verification

- Merge candidate: `4f5390107ec6ffd80a76d1d2e85530e66f21d079`, after
merging current master and the landed transport prerequisite.
Integration required no manual conflict resolution; the feature remains
99 changed files. Full workspace typecheck, production build, token
gates, and 715 focused tests passed on this merge candidate. Fresh
Greptile review is 5/5 with no unresolved findings. All 55 checks
passed, with four conditional skips, including the build, typecheck,
browser E2E, and canary dry run. A single retry recovered four jobs
interrupted by runner shutdowns; no source changes were required.
- Historical-warning UI fix: all 6,834 UI tests across 640 files passed,
including regression coverage for three old failures, legacy preserved
edits, and warnings scoped to the affected run. Full workspace
typecheck, production build, Storybook build, and token gates passed.
Browser-verified Storybook playtests passed for Historical Failures
After Successful Save, Storage Limit, and Full Storage Run Warning.
- Review follow-ups at `4e20c9fb2`: all 18 focused tests passed,
including external Git directories, linked worktrees, symlinks,
hardlinks, and distinct I/O failures alongside storage warnings. Server
and UI typechecks, token gates, and the production build passed.
- Storage warning regressions at `0724f3012`: all 33 directory tests and
all five heartbeat-list tests passed, with no skips in their successful
runs. They cover repeated runs while full, an already-over-quota saved
folder, cleanup, warnings retained after unrelated save failures, and
bounded warnings in large result JSON. Server typecheck passed after the
final warning fixes.
- Full workspace typecheck, production build, and token gates passed
during this follow-up. Product E2E harness: 631 tests passed across 52
files; harness typecheck passed. Earlier native session/context and
directory/legacy collection suites passed 537 tests; Runner
unit/transport suites passed 329 tests.
- **Real E2E at `0724f3012` (before this follow-up):** legacy local
Codex and native Daytona Codex each passed six tasks, one server
restart, seven independent assertions, and cleanup verification. Both
prove browser-to-agent edits, agent-to-browser edits, nested/binary
restoration, per-file last-sync-wins, a successful run after an
oversized save rejection, and cleanup clearing the warning.
- Native local Codex also passed the six-task quota flow before the
final warning-retention fixes. That pass began at `918d1ed02` while the
bounded-result warning fix was being edited, so it is not claimed as
exact-final-head evidence. Its final-head rerun failed during embedded
PostgreSQL bootstrap before any provider run: the macOS host had 87,365
of 87,381 SysV semaphores occupied. No unrelated services or kernel
limits were changed.
- The final-source report intentionally records **2/3 cells passed**,
preserving the blocked native-local attempt:
`tests/runner-e2e/results/agent-files-quota-final-20260928-report/`.
Earlier failed attempts and provenance notes remain under
`tests/runner-e2e/results/agent-files-quota-final-20260928-input/` and
the original campaign directories.
- Daytona used immutable image
`ghcr.io/paperclipai/paperclip-daytona-runner@sha256:5643f0d801417cae3581833a1a3bc6715b325e028602738d2652c44cac5dc6bf`
and its exact Linux runner binary. Controller source is `0724f3012`;
image source is recorded separately.
- Legacy-session compatibility and all three ACP Stop/resume browser
regressions passed on the prior validated feature head
`169fab46d5af21caa2269b4c1b29b69c933a6951`. They assert the same
provider session is retained and interrupted writes are not replayed.
Migration upgrade tests also passed earlier.
- Nine interactive stories are under **Agents / Persistent files**,
including **Full Storage Run Warning**. Its playtest and visual browser
inspection passed; the warning states that runs continue and the editor
remains available.
- Prior-head checks on `4e20c9fb2`: 55 passed, two conditional jobs
skipped, no failures or pending checks. All eight browser E2E shards and
their aggregate passed. Fresh Greptile review is 5/5 with no findings;
all review threads are resolved, the security scan passed, and GitHub
reports no merge conflicts.
- The broad local follow-up test run was interrupted after host
semaphore exhaustion affected isolated PostgreSQL instances. It also
encountered the existing macOS long-path fixture failure and two timeout
failures. This is not a claim that the full local suite passed. Logs are
retained; focused storage/warning tests passed.

## Risks

- A later sync can overwrite an earlier edit to the same file, including
a saved browser edit. There is no text merge or retained version. This
is the intended last-sync-wins policy.
- A save that exceeds a storage limit is rejected and its temporary copy
is discarded. The run itself continues normally, and later runs restore
the last saved files with a warning until cleanup. Transient sync
failures get bounded retries. An I/O failure partway through a sync can
leave some files updated; a failed receipt does not claim whole-folder
success.
- Larger folders increase copy time, network traffic, and temporary disk
usage. Active runs still need working copies. Terminal runs do not
accumulate archives. Operators must provision disk for agents and
configured concurrency; these limits are not company-wide quotas.
- A restored old native session remains instruction-only until a fresh
session starts. Its original conflict fence and existing pending
candidates remain compatible.
- Provider processes close at the collection boundary. Conversation
resume remains available, but warm process reuse is lost.
- Backups must include the instance filesystem and database. External
bundles keep their existing behavior until explicitly moved to managed
storage.

## Model Used

OpenAI Codex, GPT-6 family. The session does not expose a more specific
model ID or context-window size. Reasoning, code execution, and browser
tools assisted this change. Real provider E2E uses `gpt-5.6-sol`.

## 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: Fry (Paperclip) <noreply@paperclip.ing>

2026-09-29 08:25:56 -05:00