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## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work. > - Paperclip creates isolated instances for server-managed git worktrees. > - The worktree teardown path removes the git worktree but leaves its isolated instance directory behind. > - The leaked directory can retain an embedded PostgreSQL process and database files. > - Teardown must remove only the collision-resistant instance assigned to that exact worktree path. > - This pull request stops the verified embedded PostgreSQL process and removes the guarded instance directory. > - The benefit is complete worktree cleanup without risk to another, default, or live Paperclip instance. ## Linked Issues or Issue Description **What happened?** Closing a server-managed git worktree removed the git worktree and branch, but it left the isolated Paperclip instance directory behind. A live embedded PostgreSQL process could also keep running against that directory. **Expected behavior** Worktree teardown must stop the isolated embedded PostgreSQL process and remove only the instance assigned to that exact worktree. It must refuse mismatched instance IDs and all paths outside `PAPERCLIP_WORKTREES_DIR/instances/`. **Steps to reproduce** 1. Create a server-managed git worktree with a repo-local `.paperclip/.env` file. 2. Start its isolated embedded PostgreSQL instance. 3. Close the execution workspace. 4. Observe that the git worktree is removed but the isolated instance directory remains. **Paperclip version or commit** The bug reproduces on `master` before this change. **Deployment mode** Local development with a server-managed git worktree and embedded PostgreSQL. ## What Changed - Give server-managed worktrees collision-resistant instance IDs derived from their resolved absolute paths. - Capture the repo-local instance pointer before custom teardown commands can remove it. - Require the pointer's instance ID to match the exact worktree-derived ID. - Resolve and validate the instance path against the canonical managed worktree instance root. - Verify and stop the matching embedded PostgreSQL process before directory removal, including process-exit races. - Record successful and refused cleanup operations in the workspace operation log. - Add focused ownership, process-race, path-safety, and runtime integration tests. - Document automatic isolated-instance cleanup for server-managed worktrees. ## Verification - `pnpm --filter @paperclipai/server exec vitest run src/__tests__/workspace-instance-cleanup.test.ts` — 9 tests passed. - `pnpm --filter @paperclipai/server exec vitest run src/__tests__/workspace-runtime.test.ts -t "records teardown and cleanup operations when a recorder is provided"` — 1 test passed and 99 tests skipped. - `node scripts/__tests__/provision-worktree-self-heal.test.mjs` — 4 tests passed. - `bash -n scripts/provision-worktree.sh` — passed. - `pnpm --filter @paperclipai/server build` — passed. - `git diff --check` — passed. ## Risks The main risk is removal of the wrong instance directory. Provisioning assigns a path-derived ID with a SHA-256 suffix, and cleanup requires that exact ID in addition to a safe instance identifier, an absolute configured home, a strict child path, canonical path checks, and a second canonical path check immediately before removal. It refuses legacy or mismatched IDs, symlink escapes, and all paths outside the managed worktree instance root. Cleanup failures become visible warnings and do not delete an unverified path. > 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 with GPT-5. The runtime does not expose the exact model snapshot or context-window size. The agent used reasoning, repository tools, GitHub tools, and code execution. ## Checklist - [x] I have included a thinking path that traces from project context to this change - [x] I have specified the model used (with version and capability details) - [x] I have checked ROADMAP.md and confirmed this PR does not duplicate planned core work - [x] I have searched GitHub for duplicate or related PRs and linked them above - [x] I have either (a) linked existing issues with `Fixes: #` / `Closes #` / `Refs #` OR (b) described the issue in-PR following the relevant issue template - [x] I have not referenced internal/instance-local Paperclip issues or links (only public GitHub `#NNN` / `github.com/paperclipai/paperclip` URLs) - [x] My branch name describes the change (e.g. `docs/...`, `fix/...`) and contains no internal Paperclip ticket id or instance-derived details - [x] I have run tests locally and they pass - [x] I have added or updated tests where applicable - [x] I have updated relevant documentation to reflect my changes - [x] I have considered and documented any risks above - [x] All Paperclip CI gates are green - [x] Greptile is 5/5 with no open P2s, recommendations, or follow-ups - [x] I will address all Greptile and reviewer comments before requesting merge --------- Co-authored-by: Paperclip <noreply@paperclip.ing> Co-authored-by: Paperclip <paperclip@paperclip.ing>