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## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - Agents run tasks in isolated execution workspaces that are provisioned as git worktrees by `scripts/provision-worktree.sh` > - The script runs the base workspace's CLI (`cli/src/index.ts` via the base `tsx` install) to seed each new worktree, and it only checked that those files exist > - pnpm links each package's `node_modules` into a hash-versioned virtual store; a lockfile change followed by a partial or filtered install prunes old hashed dirs without relinking every package, leaving dangling symlinks > - A CLI with dangling symlinks fails ESM resolution (`ERR_MODULE_NOT_FOUND`) at boot, so provisioning aborts with `setup_failed` — deterministically, on every retry, with no self-heal path > - This pull request makes provisioning health-check the CLI by actually booting it, repair the base install when the check fails, and degrade to the no-CLI fallback config instead of failing the run > - The benefit is that a class of permanent `setup_failed` loops becomes self-healing, and workspace provisioning survives a broken base CLI ## Linked Issues or Issue Description No public GitHub issue exists; the underlying bug is described here per `bug_report.yml`. Related PR: #10578 self-heals the sibling workspace-validation failure loop uncovered by the same incident diagnosis. **What happened?** Isolated-workspace runs failed at provision time with `setup_failed`. Every retry failed identically. One observed incident burned 4 runs across two adapters before the task was stranded. **Expected behavior** Provisioning either succeeds or degrades gracefully; a broken base CLI install repairs itself instead of permanently blocking all new worktrees. **Steps to reproduce** In the base workspace, cause a lockfile-affecting dependency bump plus a partial/filtered `pnpm install` so a package symlink (e.g. `cli/node_modules/drizzle-orm`) dangles into a pruned virtual-store dir. Start any isolated-workspace run. Provision fails with `ERR_MODULE_NOT_FOUND` and the run ends `setup_failed`; retries never recover. **Paperclip version or commit** master as of the branch point of this PR. **Deployment mode** Local trusted deployment with git-worktree isolated workspaces. ## What Changed - `base_cli_healthy` now boots the base CLI (`--help`) instead of only testing file existence, which exercises the top-level import graph. - New `repair_base_workspace_install`: when the health check fails, run a non-interactive `pnpm install --prod=false --force --frozen-lockfile` in the base workspace. `--force` guarantees relinking when pnpm's up-to-date heuristics would skip dangling symlinks; `--frozen-lockfile` keeps the repair from mutating the shared lockfile. - The repair install is serialized with `flock` on a lock file inside the resolved git dir (`git rev-parse --absolute-git-dir`), so locking also covers base workspaces that are linked worktrees, where `.git` is a file. - If every CLI candidate is unusable (including a base CLI the repair could not fix), provisioning falls back to the existing no-CLI fallback config writer (loudly, on stderr) instead of failing the run. A CLI that runs and fails `worktree init` still fails provisioning with its real exit code — that deliberate fail-closed policy is unchanged and covered by an existing server regression test. - Fixed a latent bug: `run_isolated_worktree_init` returned 0 unconditionally after the init subshell, so callers treated a failed init as success. Exit codes now propagate. ## Verification - Reproduced the incident state (dangling `cli/node_modules/drizzle-orm` symlink); the base CLI failed with the exact `ERR_MODULE_NOT_FOUND` seen in the incident run logs. - Ran the patched script against a fresh scratch worktree: health check failed → locked repair install ran (~26 s warm) → symlink relinked → `worktree init` completed → exit 0 with `.paperclip/config.json` and `.env` written. - Happy path (healthy base CLI): provisioning behavior unchanged, exit 0. - Verified `git rev-parse --absolute-git-dir` resolves a real directory for both a normal checkout and a linked worktree. - New hermetic tests: `node --test ./scripts/__tests__/provision-worktree-self-heal.test.mjs` (4 tests: healthy CLI used, broken CLI degrades, locked repair end-to-end with a fake pnpm, init failure propagates). Not yet wired into a CI workflow. - `server`: the existing `realizeExecutionWorkspace` fail-closed regression test ("fails instead of writing an unseeded fallback config when worktree init errors after CLI detection succeeds") passes against the new script. - `bash -n scripts/provision-worktree.sh` is clean. ## Risks - Low risk overall: the script only adds recovery paths; the happy path is unchanged. - The repair install runs in the shared base workspace. It is bounded by `--frozen-lockfile` (no lockfile mutation) and serialized by `flock`, but it can add ~30 s to the first provision after a base install breaks. - If the repair cannot fix the CLI and no other CLI candidate exists, runs now continue with an unseeded fallback config instead of failing; that is intentional, and the fallback path already existed. Genuine `worktree init` failures from a working CLI still fail the run. ## Model Used Claude Fable 5 (Anthropic, model ID `claude-fable-5`), extended thinking, agentic tool use (Claude Code harness). ## 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: Claude Fable 5 <noreply@anthropic.com> Co-authored-by: Paperclip <noreply@paperclip.ing>