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## Thinking Path > - Paperclip is the open source app people use to manage AI agents for work > - A project can attach more than one repository. The task workspace keeps the selected repository at its root and puts the other project repositories under `.paperclip-repositories/<name>-<key>`, each with its own `.git` > - Agents can run on an SSH execution environment. Paperclip copies the task workspace to the remote host before the run and restores it after the run > - The SSH copy excludes `.git` at every depth, but the restore baseline excludes it only at the workspace root > - So the other project repositories reach the remote host without Git, and the restore then deletes their `.git` directories on the Paperclip host > - The next run of the same task fails during workspace setup, and the agent cannot commit to those repositories on the remote host > - This pull request transports each project repository as a Git workspace of its own, the same way the sandbox path already handles them > - The benefit is that multi-repository projects work on SSH environments across consecutive runs ## Linked Issues or Issue Description Refs #11632 (SSH workspace transfer exclude list). Related SSH workspace PRs: #14233, #14428, #14472. I found no issue or PR for this bug. **What happened?** A project has two repositories and its agent runs on an SSH environment. After the first run, the second repository under `.paperclip-repositories/` has no `.git` directory on the Paperclip host. The next run of the same task fails during setup with `Managed workspace path "…/.paperclip-repositories/<repo>" already exists but is not a git checkout.` On the remote host, `git` inside that repository resolves to the parent repository. **Expected behavior** Each project repository reaches the remote host as a Git checkout with its local changes. Remote commits and edits come back after the run. The next run of the same task starts normally. **Steps to reproduce** 1. Create a project with two repositories. 2. Configure an SSH execution environment and make it the agent's default environment. 3. Assign a task to the agent and let it run once. 4. Look at `.paperclip-repositories/<repo>` in the task workspace: `.git` is gone. 5. Wake the agent on the same task again: the run fails with `setup_failed`. **Paperclip version or commit** Reproduced on `v2026.916.1` and on `master` (`5edf55d73`). **Deployment mode** Self-hosted (Docker), authenticated, with an SSH execution environment. ## What Changed - `ssh.ts`: `prepareWorkspaceForSshExecution` lists the project repositories under `.paperclip-repositories/`. It applies the discovery rules of `readGitWorkspaceSnapshot`: each entry must be a directory with a valid name and must be a Git repository root, else the prepare step fails before any transfer. - `ssh.ts`: the anchor copy leaves `.paperclip-repositories/` out. Each project repository then gets the same import, sync, and deleted-path steps as the anchor. The remote anchor repository ignores `/.paperclip-repositories/`, as the local checkout does. - `ssh.ts`: `prepareWorkspaceForSshExecution` returns the transported repositories (the field is present only when there are repositories). `restoreWorkspaceFromSshExecution` accepts them with their baselines. It validates each path and baseline first, then restores the repositories before the anchor and stops at the first failure, as the sandbox restore does. - `remote-managed-runtime.ts`: the anchor baseline excludes `.paperclip-repositories/`, and each project repository gets its own baseline for the restore merge. - `ssh-fixture.test.ts`: regression tests for two consecutive managed runs and for the direct restore path, on a workspace with a project repository (commits, dirty edits, and a deleted file). Two tests for the new validation. - `docs/guides/board-operator/execution-workspaces-and-runtime-services.md`: one line about project repositories in the SSH round trip. ## Verification - The new regression test fails on `master` (`expected 'backend initial\n?? ../\n' to contain 'frontend initial'`) and passes with this change. - `PAPERCLIP_ENABLE_DARWIN_SSH_ENV_LAB=1 npx vitest run packages/adapter-utils/src/ssh-fixture.test.ts packages/adapter-utils/src/remote-managed-runtime.test.ts`: 32 passed, with the sshd fixture running. - `tsc --noEmit` passes for `packages/adapter-utils` and `server`, and `pnpm -r typecheck` passes for the other workspaces. The Rust step of `@paperclipai/paperclip-runner` did not run locally because `cargo` is not installed. - `node ./scripts/check-no-git-push.mjs` and `pnpm check:module-boundaries` pass. - `pnpm test:run` did not complete locally. Before it stopped, 5 tests failed: 2 in `server/src/__tests__/workspace-runtime.test.ts` and 3 in `server/src/__tests__/company-skills-service.test.ts`. The same 5 tests also fail on the base commit `5edf55d73` without this change. CI runs the full suite. - `pnpm build` passes for all workspaces except `@paperclipai/paperclip-runner` and `server`, because their build compiles the Rust runner binary and `cargo` is not installed. `tsc --noEmit` passes for `server`. - Manual test on a self-hosted `v2026.916.1` instance with the same change applied: a project with two repositories and an SSH environment. Two runs on the same task passed. After each run, the second repository keeps its `.git` on the host. On the remote host it is a Git checkout, and the remote anchor ignores it. ## Risks - Low risk. Workspaces without `.paperclip-repositories/` take the same path as before, and the return value is unchanged for them. - A workspace with an invalid entry under `.paperclip-repositories/` now fails the SSH prepare step. The sandbox path already rejects such entries. - If one repository fails to restore, the restore stops, as in the sandbox path. The remote run directory keeps the agent's work. - Each project repository adds one bundle import and one restore per run. The time grows with the number and size of the repositories. - Out of scope: other nested `.git` directories (for example a vendored checkout inside a repository) keep the existing SSH behavior. ## Model Used - Provider and model: Anthropic Claude Opus 5.5 (`claude-opus-5-5`), in Claude Code. - Capabilities: extended thinking, tool use, and code execution. The context window size was not recorded. - Use: the model investigated the bug, wrote the change and the tests, and ran the checks. A separate Claude Code agent reviewed the diff. The author reviewed the change. The manual test ran on the author's self-hosted instance. ## 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
