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DottaandPaperclip 8f1905d34d fix: provision all project repositories for local and sandbox tasks (#13442 )

## Thinking Path

> - Paperclip is the open source app people use to manage AI agents for
work.
> - Projects can now attach several source repositories.
> - Task preparation still treated these sources as alternative
workspaces.
> - Sandbox sync preserved Git history only for the selected repository.
> - A task needs every attached repository to complete work across the
project.
> - This pull request prepares all distinct project repositories and
preserves their separate Git histories through sandbox restore.

## Linked Issues or Issue Description

**What happened?**

A user reported that a project with two repositories received only the
first repository in Daytona. Repository-only project rows also reached
the agent with null local paths. Managed checkouts with matching
repository names could resolve to the same directory.

**Expected behavior**

Local and sandbox tasks receive every distinct repository attached to
their project. Repository-only sources work without preconfigured local
folders. Each repository keeps its own Git history and working files.

**Steps to reproduce**

1. Create a project with two repository sources and no local folder
paths.
2. Assign a task to the project and run it in Daytona.
3. Inspect the task workspace and the repository paths exposed to the
agent.
4. Observe that the original implementation supplies only the selected
checkout.

Related change: #13010 added multiple repository selection. The open
repository-catalog proposals #11234 and #11228 cover a different data
model. This fix uses the existing project workspaces.

## What Changed

- Materialize each additional distinct repository as an editable
checkout inside the task root. Seed configured local sources with their
current working files and retain task edits across runs.
- Pass materialized repository paths to local agents and native sandbox
task prompts. Apply existing run-scoped Git credentials to each remote
clone.
- Preserve each repository's Git history, dirty files, and restore
baseline during sandbox staging and durable recovery. Apply each
repository's ignore rules and the operator's workspace exclusions.
- Keep same-name managed repositories in separate directories. Report
additional clone failures before the task starts.
- Add task-level, checkout, sandbox round-trip, environment-hint, and
recovery-descriptor regression coverage. Document checkout and restore
behavior.

## Verification

- Red: the original implementation fails the sandbox test because the
second repository has no Git directory. It also fails the same-name
checkout test and both real-database task tests because repository hints
have no local path.
- Green: focused tests pass for one and two repository-only sources,
local source edits, clone failures, per-repository credentials, separate
Git histories, ignored files, and recovery from remote or durable seed
state.
- Live Daytona smoke passed with two disposable repositories through the
production provider sync functions. Both repositories arrived with Git
history. Commits from both restored locally. Ignored files stayed
excluded. The disposable sandbox was deleted.
- Passed on final commit `93ab76763`: `pnpm -r typecheck` and `pnpm
build`.
- Final focused coverage: 254 assertions across the six changed test
areas passed across the serial run and an isolated rerun of the existing
process-kill timing test. The live Daytona smoke also passed.
- The local `pnpm test:run` overlapped source edits and retained stale
transformed code. Its first phase reported 12,240 passed assertions,
nine failed assertions, three hook failures, and one worker error; later
phases did not run locally. This run is not claimed as green. Fresh
focused tests verify the changes, and every general/workspace and
serialized-server CI shard passes on the final commit.
- Final CI is green on `93ab76763`: all test shards, all three browser
shards, typecheck, build, runner verification, canary dry run, and
security checks. The initial unrelated chat-delivery browser timing
failure passed in the final CI run. Optional Storybook visual checks
were skipped.
- Greptile is 5/5 on the final commit with no unresolved review threads.
Its checkout-race finding was reproduced with a failing test, fixed, and
rechecked.

## Risks

- Additional repositories need disk space and clone time. Access failure
for an attached repository stops preparation.
- Additional checkouts live under `.paperclip-repositories/` and keep
independent histories. Changes stay in those task copies; they do not
overwrite configured source folders.
- Detached or reconfigured repository copies are retained under
`.paperclip-runtime/detached-repositories/`. Sandbox recovery retains
per-repository merge baselines.
- No database migration, UI contract change, or new credential
delegation is required. Referenced projects retain their separate
read-only behavior.

## Model Used

OpenAI Codex, based on GPT-6, with repository inspection, code
execution, and tool use. The runtime does not expose a more specific
model deployment ID or context-window size.

## 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>

2026-09-14 18:37:51 -05:00

src

fix: provision all project repositories for local and sandbox tasks (#13442 )

2026-09-14 18:37:51 -05:00

CHANGELOG.md

fix: bound workspace Git scans (#11572 )

2026-08-17 22:11:30 -05:00

package.json

feat(connections): add self-serve intent runtime (#12345 )

2026-08-29 12:08:34 -05:00

README.md

…

tsconfig.json

…

README.md

@paperclipai/adapter-utils

Shared utilities for Paperclip adapters: process spawning, environment injection, sandbox/SSH transport, workspace sync, and the round-trip helpers that move code between the local execution-workspace cwd and wherever the agent actually runs.

For the adapter-author guide see docs/adapters/creating-an-adapter.md and the in-repo notes at packages/adapters/AUTHORING.md.

No-remote-git contract

The local execution-workspace cwd is the only persistence boundary across runs. No adapter may depend on a git remote for cross-run state.

Adapters that run the agent on a different host should use the SSH round-trip helpers in src/ssh.ts:

prepareWorkspaceForSshExecution({ spec, localDir, remoteDir }) — bundles the local cwd (tracked files, dirty edits, untracked additions, and the git history needed to reconstruct it) to remoteDir before the run starts. Runs with no git remote configured.
restoreWorkspaceFromSshExecution({ spec, localDir, remoteDir, ... }) — syncs the remote cwd back into localDir after the run, including any new commits the agent created. Also runs with no git remote configured.

prepareRemoteManagedRuntime in src/remote-managed-runtime.ts wraps both calls for adapters that want a per-run remote workspace and an automatic restoreWorkspace() finally hook.

The invariant is pinned by the no-remote-git contract case in src/ssh-fixture.test.ts, which asserts that a remote-only commit propagates to the local worktree through the prepare → restore round-trip with no git remote configured at any point. Do not regress that test.