fix: refresh remote PR worktree bases

[shixi-li]

Summary

Explicit PR bases were passed to Git as local short refs, so a stale local branch could change the worktree start commit even when the remote branch was current.

Related Issues

Fixes #711

Changes Made

• fetch explicit PR bases into a unique temporary ref without updating shared remote-tracking refs or FETCH_HEAD
• resolve the exact temporary ref to a commit before creating the worktree, then clean it up without masking the original result
• require fresh remote data only for explicit PR bases while preserving cached offline behavior for repository worktree settings
• cover foreground and detached-derived starts, short-ref collisions, shared-ref lock contention, fetch failure, and temporary-ref cleanup

Testing

• node tests/run-tests.js tests/integration/worktree-isolation.test.js --timeout 30000 --jobs 1 (28 passing)
• relevant orchestrator, detached-startup, and PR-base tests (94 passing, 1 pending)
• npm run check
• Prettier on all changed files
• npm run test:all
• npm audit --omit=dev --audit-level=high
• git diff --check origin/dev...HEAD

Checklist

• Tests pass (npm test)
• Documentation updated (not needed for this behavior-only fix)
• Follows commit guidelines

[greptile-apps]

Greptile Summary

Refreshes explicit PR worktree bases without mutating shared Git refs.

• Fetches the requested remote branch into a unique temporary ref and resolves its commit before worktree creation.
• Cleans up temporary refs on success and failure while preserving cached behavior for repository-configured bases.
• Passes explicit PR bases through the fresh-fetch path and adds coverage for contention, stale refs, failures, and cleanup.

Confidence Score: 5/5

The PR appears safe to merge.

No blocking failures remain in the fix associated with the previous review thread.

Important Files Changed

Filename	Overview
src/isolation-manager.js	Fetches explicit PR bases through isolated temporary refs, creates worktrees from resolved commits, and reliably attempts temporary-ref cleanup.
src/orchestrator.js	Routes explicit PR bases to refreshed origin refs and records the resolved worktree base commit.
tests/integration/worktree-isolation.test.js	Adds integration coverage for fresh PR bases, shared-ref contention, fetch failures, immutable base selection, and temporary-ref cleanup.
tests/orchestrator.test.js	Updates orchestrator expectations for origin-qualified PR bases and mandatory fresh fetching.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  A[Explicit PR base] --> B[Fetch remote branch]
  B --> C[Unique temporary ref]
  C --> D[Resolve immutable commit SHA]
  D --> E[Create worktree from SHA]
  E --> F[Delete temporary ref]

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_{Reviews (3): Last reviewed commit: "chore: sync latest dev fix" | Re-trigger Greptile}