[Bil0000]

Deleting a thread left its Git checkpoint refs behind, which cluttered Git tools and kept old snapshot data reachable. Deletion now queues cleanup after checkpoint writes, removes only that thread's old and current refs, and handles removed worktrees through the project repo. Archived threads keep their restore history.

Addresses #13263 (comment).

Related bug report: #24083.

Verified with failing regression tests before the fix, real Git tests for packed refs, shared worktrees and lock failures, a capture-order test, and vp run check:changed.

Refs from threads deleted before this change need manual cleanup. Git's normal maintenance reclaims the unused data.

Built with GPT-6.1 Sol high/priority in the Codex harness, with Astra high design and review.

[macroscopeapp]

Approvability

Verdict: Needs Human Approval

Macroscope's review found this PR requires human approval — This PR adds checkpoint cleanup to thread deletion across worktrees and project repositories, including new outbox sequencing and atomic Git ref deletion. The behavior is well-tested but cross-cutting and destructive on an existing production path, warranting human review.

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[coderabbitai]

No actionable comments were generated in the recent review.

Recent review info

Run configuration

• Source mode: Auto
• Repository: pingdotgg/t3code
• Branch: main
• File: .coderabbit.config.ts
• Commit: c5332bf
• Layers: Repository TS config
• Review profile: CHILL
• Plan: Advanced
• Run ID: 0c596514-9dbb-4a0f-afa4-9089d2d2a488

Commits

Reviewing files that changed from the base of the PR and between c5332bf and 541e43b.

Files selected for processing: 19

• apps/server/src/checkpointing/CheckpointStore.test.ts
• apps/server/src/checkpointing/CheckpointStore.ts
• apps/server/src/checkpointing/Utils.ts
• apps/server/src/guest/GuestShareService.test.ts
• apps/server/src/orchestration-v2/CheckpointCaptureService.test.ts
• apps/server/src/orchestration-v2/CheckpointCaptureService.ts
• apps/server/src/orchestration-v2/CheckpointService.ts
• apps/server/src/orchestration-v2/EffectOutbox.ts
• apps/server/src/orchestration-v2/EffectWorker.ts
• apps/server/src/orchestration-v2/ResourceCleanupService.test.ts
• apps/server/src/orchestration-v2/ResourceCleanupService.ts
• apps/server/src/orchestration-v2/RunFinalizationQueue.test.ts
• apps/server/src/orchestration-v2/ThreadDeletion.test.ts
• apps/server/src/orchestration-v2/ThreadDeletion.ts
• apps/server/src/orchestration-v2/runtimeLayer.test.ts
• apps/server/src/orchestration-v2/runtimeLayer.ts
• apps/server/src/project/ProjectService.deletion.test.ts
• apps/server/src/vcs/GitVcsDriver.ts
• apps/server/src/vcs/VcsDriver.ts

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Walkthrough

Thread deletion now queues checkpoint-ref cleanup. The cleanup service removes matching refs from relevant Git repositories. Git validates and deletes explicit refs and prefix matches atomically. Checkpoint capture now returns early for deleted threads.

Changes: Checkpoint Cleanup

Layer / File(s)	Summary
Checkpoint ref deletion apps/server/src/checkpointing/*, apps/server/src/orchestration-v2/CheckpointService.ts, apps/server/src/vcs/*	The deletion input accepts ref prefixes. Thread and scope prefix helpers provide ref paths. Git validates refs and prefixes, expands matching refs, and deletes the collected refs in one transaction. Tests cover exact and prefix deletion, repeated calls, locked refs, invalid inputs, and preservation of unrelated refs.
Deleted thread cleanup apps/server/src/orchestration-v2/ResourceCleanupService.ts, apps/server/src/orchestration-v2/ResourceCleanupService.test.ts, apps/server/src/orchestration-v2/runtimeLayer.ts, apps/server/src/orchestration-v2/runtimeLayer.test.ts	ResourceCleanupService skips cleanup for threads that are not deleted. For deleted threads, it checks relevant directories and removes matching refs from existing repositories. The service dependencies and tests are updated.
Deletion effect and capture handling apps/server/src/orchestration-v2/{EffectOutbox.ts,EffectWorker.ts,ThreadDeletion.ts,ThreadDeletion.test.ts,RunFinalizationQueue.test.ts,CheckpointCaptureService.ts,CheckpointCaptureService.test.ts}, apps/server/src/project/ProjectService.deletion.test.ts, apps/server/src/guest/GuestShareService.test.ts	Thread deletion plans a replay-safe checkpoint.cleanup effect, and the effect worker calls the cleanup service. Tests cover effect ordering and project deletion. Checkpoint capture returns early for deleted threads, with test coverage for deleted and rolled-back runs.

Priority: Low

Estimated code review effort: 3 (Moderate) | ~25 minutes

Change: Bug fix

Sequence Diagram(s)

sequenceDiagram
  participant ThreadDeletion
  participant EffectOutbox
  participant EffectWorker
  participant ResourceCleanupService
  participant GitVcsDriver
  ThreadDeletion->>EffectOutbox: enqueue checkpoint.cleanup
  EffectOutbox->>EffectWorker: provide cleanup effect
  EffectWorker->>ResourceCleanupService: cleanupCheckpointRefs(threadId)
  ResourceCleanupService->>GitVcsDriver: deleteCheckpointRefs(prefixes)

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Possibly related issues

• [Bug]: Checkpoint refs are never pruned and make git fetch slow enough to break Claude thread starts #24083: The issue describes unpruned checkpoint refs after thread deletion; this change adds cleanup for deleted threads’ checkpoint refs.

Suggested labels: bugfix, size:L

Suggested reviewers: yash-singh1, maria-rcks, juliusmarminge

Merge Risk: Minimal · up to 541e4

Thread deletion can proceed with checkpoint-ref cleanup; no issue identified here prevents merging after normal checks.

Pre-merge checks: 3 · 1

Failed checks: 1 warning

Check name	Status	Explanation	Resolution
Description check		The description explains the problem and change, links the related discussion and bug report, and lists focused verification. It does not provide the explicit maintainer approval required by the Scope…	Add the maintainer’s explicit approval of the change’s direction and scope, including the approval comment. Also state the observed results of the verification checks.

Passed checks: 3 passed

Check name	Status	Explanation
Title check		The title clearly and concisely describes the main change: removing checkpoint refs when threads are deleted.
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

Full details: Description check

Explanation

The description explains the problem and change, links the related discussion and bug report, and lists focused verification. It does not provide the explicit maintainer approval required by the Scope and approval section.

Resolution

Add the maintainer’s explicit approval of the change’s direction and scope, including the approval comment. Also state the observed results of the verification checks.

Finishing Touches

🧪 Generate unit tests (beta)

• Create a new PR

• Autofix · Keep fixing CodeRabbit findings and required CI, and resolving merge conflicts

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[juliusmarminge]

Taking over this one

[juliusmarminge]

Thanks @Bil0000 for identifying the checkpoint-ref leak and establishing the reproduction, scoped deletion, and archived-history requirements. Rebuilt this as #25182: a durable cleanup payload, bounded Git ref deletion, and cleanup that retries after lock contention and restart without blocking other resource cleanup. I compared the original diff against the replacement; legacy and current refs, removed-worktree fallback, capture ordering, and project deletion are covered. The original test collection was replaced with focused behavioral regressions and isolated before/after server proof. Closing this in favor of the credited replacement.