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Devin FoleyandPaperclip
f3a214fe77
## Thinking Path > - Paperclip manages agents and their task workspaces. > - A task can use several independent Git repositories. > - Sandbox staging copies secondary repositories from temporary clones. > - The copy changed relative symlinks into absolute host paths. > - Those links broke skill discovery and made workspace restore fail. > - This change preserves link targets while keeping extraction checks intact. ## Linked Issues or Issue Description **What happened?** Staging a secondary repository rewrites a link such as `.claude/skills/demo -> ../../skills/demo` to an absolute path in a temporary Git clone. That clone is then removed. The link is broken in the sandbox, and Daytona refuses the outbound archive during workspace restore. An agent can finish its turn but still have its run fail during restore. **Expected behavior** Repository links keep their original targets after staging. Links within a repository remain usable, and changes return to the local checkout. Unsafe outbound archive links still fail before extraction. **Steps to reproduce** 1. Create a project with a primary repository and a secondary repository. 2. Commit a relative skill directory link in the secondary repository. 3. Stage the workspace for sandbox execution and inspect the copied link. 4. Restore that repository through Daytona. Before this fix, the link points at a removed host temporary directory and restore rejects it. **Paperclip version/commit** Reproduced on `0f8750627f11d855552abce9a837d7f3b67c9ddf` in the multi-repository sandbox path. Related: #13442 introduced multi-repository provisioning. #13882 adds native Grok but keeps legacy adapters; #12991 addresses Grok instruction isolation and leaves skill staging unchanged. Searches of open/closed PRs and open issues found no direct fix for this copy behavior. ## What Changed - Set `verbatimSymlinks: true` when copying secondary Git clones. This [Node option](https://nodejs.org/api/fs.html#fspromisescpsrc-dest-options) preserves the stored link target instead of resolving it against the temporary source. - Test directory, file, chained and dangling links after temporary-clone cleanup. Assert the copied Git checkout remains clean. - Cover skill-link reads, edits and restore in fresh, warm-adoption and durable-seed workspace modes. - Extend Daytona checks for valid relative directory links and rejected absolute targets. - Document the staging behavior. ## Verification - Four regression cases fail without the source fix: one clone test and three staging modes. - `pnpm exec vitest run packages/adapter-utils/src/git-workspace-sync.test.ts packages/adapter-utils/src/sandbox-managed-runtime.test.ts packages/plugins/sandbox-providers/daytona/src/plugin.test.ts`: 301 passed. - `pnpm -r typecheck` and `pnpm build`: passed. - `pnpm test:run` was started locally, then stopped after the full Linux CI suite passed. It did not finish locally; this is not a full local-suite pass. - Full PR CI: 53 checks passed, two conditional skips, on `07b30ff298baab327a4e60708ade899935688a3f`. Three server shards were interrupted by runner shutdowns; the unchanged mobile repository test timed out waiting for a disabled Save changes button. One same-commit failed-job rerun passed. Original attempts remain in [run 36036538369](https://github.com/paperclipai/paperclip/actions/runs/36036538369). - Greptile: 5/5 on the same head, no review threads or actionable findings. - Diff scanned for secrets and private identifiers; no matches. ## Risks Low risk: the production change is one copy option. It preserves symlinks instead of following or materializing their targets. Daytona extraction guards, workspace exclusions, authentication and database behavior do not change. This prevents corruption in newly staged snapshots. It does not rewrite an already corrupted warm workspace or durable seed; those need fresh staging from the source checkout. No live provider run or customer-task replay was performed. The tests use real Git, filesystem and tar operations with mocked provider transport. ## Model Used OpenAI GPT-6 through Codex, with tool use and code execution. The exact serving model identifier and context-window size 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 `#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>