## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work.
> - The CLI test suite uses embedded Postgres for worktree checks.
> - Several tests start a cluster and run migrations on each test.
> - Runner contention can make this cost class exceed small hand-written
time budgets.
> - A timed-out test can also leave the cluster alive while cleanup
removes its data directory.
> - This pull request gives the cost class one measured timeout and
registers cleanup for the timeout path.
> - The benefit is stable tests and fewer orphaned embedded Postgres
processes.
## Linked Issues or Issue Description
No public GitHub issue tracks this defect. Related PRs #10987 and #10961
address wider embedded-Postgres test setup issues. This pull request
addresses the CLI timeout and cleanup path described below.
**What happened?**
Five CLI tests used different hand-written time budgets while they
started embedded Postgres and ran migrations. Runner contention made one
test exceed its budget. A timeout also skipped the `finally` cleanup
path and left a Postgres process alive.
**Expected behavior**
Each embedded-Postgres test gets a budget that covers measured runner
contention. Cleanup stops the cluster before the test removes its data
directory, including after a timeout.
**Steps to reproduce**
1. Run `npx vitest run cli/src/__tests__/worktree.test.ts` on a
contended runner.
2. Observe the embedded-Postgres tests take longer than their small
hand-written budgets.
3. Inspect the process list after a timeout and observe an orphaned
Postgres process.
**Paperclip version or commit**
The defect reproduces on `master` before this pull request.
**Deployment mode**
Built from source with Vitest.
**Installation method**
Built from source with pnpm.
## What Changed
- Export `EMBEDDED_POSTGRES_TEST_TIMEOUT_MS` from the embedded-Postgres
test helper.
- Apply the shared timeout to every test defined by
`itEmbeddedPostgres`.
- Replace the five hand-written timeout values in `worktree.test.ts`.
- Register temporary-directory removal and cluster stop with
`onTestFinished` in the correct order.
- Restore the working directory during timeout cleanup.
## Verification
- `npx vitest run cli/src/__tests__/worktree.test.ts` passes 63 tests.
- `npx vitest run cli/src` passes 424 tests across 59 files.
- `tsc --noEmit` in `cli/` adds no new error in the touched files.
- CI must pass on the pull request head.
- Greptile must report 5/5 with no unresolved blocking thread.
## Risks
- Low risk. The change affects test helpers and test cleanup only.
- The shared budget can lengthen a failing test before Vitest reports
the failure.
- The cleanup order depends on Vitest callback order, which the tests
now use explicitly.
## Model Used
OpenAI Codex, GPT-5. The model used tool calls and code review support.
The context window size and internal reasoning mode were not exposed in
this run.
## 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>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Paperclip uses database clients and embedded PostgreSQL test
fixtures
> - A fixture stopped its embedded PostgreSQL cluster while clients
still held connections
> - The postgres.js driver then scheduled a write on a stopped
connection
> - That write escaped the timer callback and caused a test process to
exit with an error
> - This pull request closes registered clients before the fixture stops
its cluster
> - The benefit is stable test teardown and clear failure reporting in
continuous integration
## Linked Issues or Issue Description
Refs: #10869
**What happened?**
An embedded PostgreSQL test fixture stopped its cluster while database
clients still held open connections. The postgres.js driver then
scheduled a deferred write on a dead connection. The write caused an
unhandled error after the test shard reported success.
**Expected behavior**
The fixture closes all live clients for its cluster before it stops the
embedded PostgreSQL cluster. Tests then finish without a deferred write
on a dead connection.
**Steps to reproduce**
1. Run the database regression test with the embedded PostgreSQL
fixture.
2. Stop the fixture while its database client still has an open
connection.
3. Observe the deferred write and the process exit status.
**Paperclip version or commit**
Branch base: bdd8f1bed. Change head:
93e85d2ba1.
**Deployment mode**
Local dev with the embedded PostgreSQL test fixture.
**Installation method**
Built from source with pnpm.
**Agent adapter(s) involved**
Not adapter-specific. This change covers database test infrastructure.
**Database mode**
Embedded PGlite.
**Additional context**
The change keeps client references weak and keys them by host and port.
It does not retain credentials. It also handles connection URLs that the
driver accepts when the URL parser rejects them.
## What Changed
- Add a registry for live database clients in the database package.
- Close registered clients before the embedded PostgreSQL fixture stops
its cluster.
- Add a regression test for the teardown race.
- Handle driver-compatible URLs that the standard URL parser rejects.
- Add cleanup for the shared route test harness.
## Verification
- Run the full `packages/db` suite.
- Run `tsc --noEmit` in `packages/db`.
- Run the server suite that uses `route-test-harness.ts`.
- Run the teardown regression test five times.
- Confirm that the negative control fails three times.
- Confirm that no shard reports green tests and exits with an error.
## Risks
The registry changes client cleanup for embedded test fixtures. Weak
references limit retained memory in long-lived processes. The registry
uses host and port only, so it does not retain credentials. No
migration, schema, API, telemetry, authentication, or cryptography
change exists.
## Model Used
OpenAI Codex, GPT-5, tool use and code review support, standard
reasoning mode. The implementing engineer supplied the code and
verification results.
## 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>
## Thinking Path
> - Paperclip manages agent work in isolated execution workspaces.
> - A workspace depends on a valid database seed before it can run.
> - Deferred seed failures were hidden behind a successful provision
status.
> - The seed restore also had two possible owners for the embedded
PostgreSQL process.
> - That allowed the target database to stop while the restore was still
running.
> - This pull request makes seed failures visible and gives the seed
process sole lifecycle ownership.
> - The benefit is that workspace provisioning reports the real result
and does not stop its own target database.
## Linked Issues or Issue Description
Related: #11684
**What happened?**
Initial worktree provisioning could report success before its deferred
database seed completed. The seed restore could also reuse a target
embedded PostgreSQL process with another shutdown owner. This could stop
the target database during the restore.
**Expected behavior**
Workspace status must show a failed deferred seed as a failure. The seed
restore must own the target embedded PostgreSQL process until restore,
migration, and validation finish.
**Steps to reproduce**
1. Provision a worktree with deferred database seeding.
2. Make the seed manifest end in a failed state while the command exits
with code 0.
3. Observe that the provision status remains successful on `master`.
4. Start a seed restore against an already-running target embedded
PostgreSQL process.
5. Observe that another lifecycle owner can stop the target during
restore.
**Paperclip version or commit**
`51a843e135`
**Deployment mode**
Local dev with execution workspaces and embedded PostgreSQL.
## What Changed
- Add a first-class `workspace_seed` operation for deferred database
seeds.
- Require terminal, verified seed evidence before the seed operation
succeeds.
- Surface the seed phase and failure metadata in workspace status and UI
state.
- Give the seed process exclusive lifecycle ownership of the target
embedded PostgreSQL process.
- Suppress imported embedded-Postgres exit hooks without removing
existing host listeners.
- Record a credential-safe shutdown diagnostic in failed seed manifests.
## Verification
- The original deferred-seed commit passed 4 server tests, 24
workspace-status UI tests, shared/server/UI typechecks, and the UI token
gate.
- The original PostgreSQL-lifecycle commit passed 3 lifecycle tests, 3
ownership/diagnostic tests, 1 real embedded-Postgres seed integration,
and the affected package typechecks.
- No local tests were rerun after the clean cherry-pick because the
operator requested the shortest landing path.
- Review the automatic PR checks for the clean `origin/master` replay.
## Risks
- A live target database now causes an early error instead of being
reused. The error includes recovery guidance.
- Workspace consumers must handle the new `workspace_seed` operation
type. Shared types and UI state handling are updated in this pull
request.
> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.
## Model Used
- OpenAI Codex, GPT-5, high-reasoning mode, with repository, shell, and
GitHub tool use. The runtime does not expose a more specific deployment
suffix or context-window value.
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have searched GitHub for duplicate or related PRs and linked
them above
- [x] I have either (a) linked existing issues with `Fixes: #` / `Closes
#` / `Refs #` OR (b) described the issue in-PR following the relevant
issue template
- [x] I have not referenced internal/instance-local Paperclip issues or
links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip`
URLs)
- [x] My branch name describes the change (e.g. `docs/...`, `fix/...`)
and contains no internal Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip is the open source app people use to manage AI agents for
work
> - Governed MCP access spans contracts, runtime enforcement, adapters,
UI surfaces, and operator verification
> - The parity reference PR #9534 is too large for effective automated
or human review
> - The feature therefore needs a linear stack whose individual diffs
stay below the 100-file review limit
> - This pull request is split 2/8 and focuses on database schema and
shared governance contracts
> - The benefit is a standalone, testable review boundary while
preserving byte-for-byte parity at the top of the stack
## Linked Issues or Issue Description
- Related parity reference: #9534
- Problem: The governed access model needs additive persistence and
synchronized shared types before server enforcement can compile.
- Proposed solution: Adds migrations 0148–0169, tool-access and Smoke
Lab schema, shared types/validators/gallery helpers, and the minimal
compile-required contract consumers identified by boundary testing.
- Alternatives considered: keeping #9534 as one 403-file review, or
rewriting the feature to manufacture seams; both were rejected in favor
of path extraction plus compile-driven boundary moves.
- Roadmap alignment: this advances the existing governed MCP/tool-access
work already represented by #9534; it does not introduce a separate
roadmap initiative.
- Stack position: base branch is `pap10341-split/01-demo-servers`.
- Merge policy: merge bottom-up, in order, only after the complete
eight-PR stack has been reviewed and the top-of-stack parity gate
remains empty.
- Requested review: QA for migrations/validators; Greptile on every PR.
## What Changed
- Adds migrations 0148–0169, tool-access and Smoke Lab schema, shared
types/validators/gallery helpers, and the minimal compile-required
contract consumers identified by boundary testing.
- Keeps this PR below 100 changed files and independently typecheckable.
- Preserves the final tree from #9534 when combined with the other seven
stack levels.
## Verification
- `pnpm typecheck` — passed, including migration numbering and safety
checks
- `pnpm --filter @paperclipai/db test` — passed
- `pnpm --filter @paperclipai/shared test` — passed
## Risks
- Migration or contract mistakes could affect every upper layer; all
migrations are additive/idempotent and compile consumers are included in
this boundary.
- Stack risk: merging out of order can expose incomplete layers;
mitigate by following the documented bottom-up merge policy.
- Parity risk: later edits to an intermediate branch can drift from
#9534; mitigate by re-running the empty top-of-stack diff before merge.
> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.
## Model Used
- OpenAI Codex, exact model ID `gpt-5.4`; runtime-managed context
window; medium reasoning with repository, shell, Git, GitHub CLI, and
code-execution tools enabled.
## 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] Internal references are omitted except the execution-plan link
explicitly required for this coordinated split stack
- [x] My branch name describes the change and contains no internal
Paperclip ticket id or instance-derived details
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [ ] All Paperclip CI gates are green
- [ ] Greptile is 5/5 with no open P2s, recommendations, or follow-ups
- [x] I will address all Greptile and reviewer comments before
requesting merge
## Stack Coordination
- Internal execution plan:
[PAP-13874](/PAP/issues/PAP-13874#document-plan)
- Parity reference: #9534
- Stack: #9556 → #9557 → #9558 → #9559 → #9560 → #9561 → #9562 → #9563
- Merge bottom-up only after full-stack review and an empty parity diff
at #9563.
---------
Co-authored-by: Paperclip <noreply@paperclip.ing>
## Thinking Path
> - Paperclip coordinates autonomous company work through local and
hosted runtime surfaces.
> - Local embedded Postgres and tenant import/export paths are
foundational reliability pieces.
> - A runtime failure in either path can stop agents or imports before
useful work begins.
> - The branch included remaining fixes for embedded native library
bootstrap and async tenant import handling.
> - This pull request groups those runtime/import reliability changes
into one standalone PR.
> - The benefit is a more robust local runtime and safer cloud tenant
import behavior.
## What Changed
- Prepared embedded Postgres native runtime before startup in
CLI/server/test entrypoints.
- Added embedded Postgres native bootstrap coverage.
- Added async tenant import job handling and deferred validation
coverage.
- Kept the runtime/import changes based directly on current
`origin/master` after related upstream PRs had already merged.
## Verification
- `pnpm --filter @paperclipai/plugin-sdk build`
- `NODE_ENV=test pnpm exec vitest run
packages/db/src/embedded-postgres-native.test.ts
server/src/__tests__/company-portability-routes.test.ts`
## Risks
- Medium-low: this touches startup/import paths, but the branch is small
and covered by targeted tests.
- The embedded Postgres change depends on platform-specific
native-library behavior, so CI and follow-up checks should still verify
supported runners.
> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.
## Model Used
- OpenAI GPT-5 Codex via `codex_local`, tool-enabled coding session;
exact context window not exposed by this runtime.
## Checklist
- [x] I have included a thinking path that traces from project context
to this change
- [x] I have specified the model used (with version and capability
details)
- [x] I have checked ROADMAP.md and confirmed this PR does not duplicate
planned core work
- [x] I have run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
## Thinking Path
> - Paperclip orchestrates AI agents for zero-human companies.
> - Operators and agents coordinate through company-scoped issues,
comments, documents, and task relationships.
> - Issue text can mention other tickets, but those references were
previously plain markdown/text without durable relationship data.
> - That made it harder to understand related work, surface backlinks,
and keep cross-ticket context visible in the board.
> - This pull request adds first-class issue reference extraction,
storage, API responses, and UI surfaces.
> - The benefit is that issue references become queryable, navigable,
and visible without relying on ad hoc text scanning.
## What Changed
- Added shared issue-reference parsing utilities and exported
reference-related types/constants.
- Added an `issue_reference_mentions` table, idempotent migration DDL,
schema exports, and database documentation.
- Added server-side issue reference services, route integration,
activity summaries, and a backfill command for existing issue content.
- Added UI reference pills, related-work panels, markdown/editor mention
handling, and issue detail/property rendering updates.
- Added focused shared, server, and UI tests for parsing, persistence,
display, and related-work behavior.
- Rebased `PAP-735-first-class-task-references` cleanly onto
`public-gh/master`; no `pnpm-lock.yaml` changes are included.
## Verification
- `pnpm -r typecheck`
- `pnpm test:run packages/shared/src/issue-references.test.ts
server/src/__tests__/issue-references-service.test.ts
ui/src/components/IssueRelatedWorkPanel.test.tsx
ui/src/components/IssueProperties.test.tsx
ui/src/components/MarkdownBody.test.tsx`
## Risks
- Medium risk because this adds a new issue-reference persistence path
that touches shared parsing, database schema, server routes, and UI
rendering.
- Migration risk is mitigated by `CREATE TABLE IF NOT EXISTS`, guarded
foreign-key creation, and `CREATE INDEX IF NOT EXISTS` statements so
users who have applied an older local version of the numbered migration
can re-run safely.
- UI risk is limited by focused component coverage, but reviewers should
still manually inspect issue detail pages containing ticket references
before merge.
> For core feature work, check [`ROADMAP.md`](ROADMAP.md) first and
discuss it in `#dev` before opening the PR. Feature PRs that overlap
with planned core work may need to be redirected — check the roadmap
first. See `CONTRIBUTING.md`.
## Model Used
- OpenAI Codex, GPT-5-based coding agent, tool-using shell workflow with
repository inspection, git rebase/push, typecheck, and focused Vitest
verification.
## 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 run tests locally and they pass
- [x] I have added or updated tests where applicable
- [x] If this change affects the UI, I have included before/after
screenshots
- [x] I have updated relevant documentation to reflect my changes
- [x] I have considered and documented any risks above
- [x] I will address all Greptile and reviewer comments before
requesting merge
---------
Co-authored-by: dotta <dotta@example.com>
Co-authored-by: Paperclip <noreply@paperclip.ing>
Replace single retentionDays with a three-tier BackupRetentionPolicy:
- Daily: keep all backups (presets: 3, 7, 14 days; default 7)
- Weekly: keep one per calendar week (presets: 1, 2, 4 weeks; default 4)
- Monthly: keep one per calendar month (presets: 1, 3, 6 months; default 1)
Pruning sorts backups newest-first and applies each tier's cutoff,
keeping only the newest entry per ISO week/month bucket. The Instance
Settings General page now shows three preset selectors (no icon, matches
existing page design). Remove Database icon import.
Add agent_config_revisions table for tracking agent configuration changes with
rollback support. Add issue_approvals junction table linking issues to approvals.
New migrations (0005, 0006) for permissions column and new tables. Rework migration
client with statement-level idempotency checks (table/column/index/constraint
existence) so migrations can be safely retried against partially-migrated databases.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add issuePrefix/issueCounter to companies and issueNumber/identifier to issues
for human-readable issue IDs (e.g. PAP-42). Add runId to activity_log for
linking activity to heartbeat runs. Rework DB client to support migration
state inspection and interactive pending migration prompts at startup.
Add reopen option to issue comments validator.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Switch from PGlite (WebAssembly) to embedded-postgres for zero-config
local development — provides a real PostgreSQL server with full
compatibility. Add startup banner with config summary on server boot.
Improve server bootstrap with auto port detection, database creation,
and migration on startup. Update DATABASE.md, DEVELOPING.md, and
SPEC-implementation.md to reflect the change. Update CLI database
check and prompts. Simplify OnboardingWizard database options.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Add @electric-sql/pglite so the server can run without an external
Postgres instance. When DATABASE_URL is not set, the server auto-creates
an embedded PGlite database in ./data/pglite with schema push on startup.
- Add createPgliteDb() alongside the existing createDb()
- Make DATABASE_URL optional in server config
- Update drizzle config to glob schema files
- Update migrate script to support both Postgres and PGlite
- Add data/ to .gitignore for local PGlite storage
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Postgres schema via Drizzle ORM for agents, goals, issues, projects,
and activity log tables. Includes migration runner, seed script,
and Drizzle config.
Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>
Nicky Leach
Dotta
Aron Prins
dotta
Dotta
Forgotten