Replace git worktrees with local clones for complete agent isolation#153
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that-github-user merged 1 commit intomainfrom Mar 29, 2026
Merged
Replace git worktrees with local clones for complete agent isolation#153that-github-user merged 1 commit intomainfrom
that-github-user merged 1 commit intomainfrom
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Root cause: agents with Bash access discover the main repo via worktree .git pointer files, then run git worktree commands that destroy other agents' metadata. Locks, backups, gc.auto=0, and prompt constraints all failed because agents are creative at finding the main repo. Fix: use plain git clone instead of git worktree add. Local clones use hardlinks (near-zero extra disk), have fully independent .git directories, and share no metadata with the main repo or other clones. An agent can rm -rf .git, git init, or run any git command without affecting anything outside its own clone. Verified: 3/3 Opus agents on our own repo captured diffs successfully. Zero ENOENT errors. 89% convergence. The getDiff bug is fixed. Research: evaluated --shared (alternates risk), --dissociate (unnecessary overhead), worktree hybrid (complexity). Plain local clone wins on all axes: isolation, speed (0.1s), disk (hardlinks), and simplicity. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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…ments' We switched from worktrees to clones in #153 but the user-facing messages still said 'worktrees'. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Summary
Replace
git worktree addwithgit clone(local, hardlinks) for agent isolation.Root cause: Agents discover the main repo via .git pointer files and run destructive git worktree commands. All mitigations (locks, backups, gc.auto=0, prompt constraints) failed.
Fix: Local clones have fully independent .git directories. No shared metadata. No path to main repo. Near-zero disk overhead via hardlinks.
Verified: 3/3 Opus agents on our own repo captured diffs successfully. Zero ENOENT errors. 89% convergence.
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