[josephv123]

Problem

A worktree T3 creates for a thread stays "racily clean" until something outside T3 rewrites its index, and until then every checkpoint capture and every status refresh in it re-reads the whole checkout (#21328).

git worktree add writes the files first and the index last. Git re-reads, on every status, diff and add, each file whose mtime falls in the index's own second or later. With the checkout.workers=0 that createWorktree passes, a t3code checkout (28,271 files, 396 MB) finishes in about 0.63 s here, so often all of it lands in that second. Nothing T3 runs ever writes the index:

• status polling uses GIT_OPTIONAL_LOCKS=0 and plumbing diff-index (fix(server): status polling no longer locks the git index #14718);
• captures work on a copy of the index;
• the agents don't either: Claude Code's startup commands use --no-optional-locks, and Codex's startup left the index unwritten too.

Numbers from #21328, measured in such a worktree:

	fresh worktree	after one git update-index -q --refresh
Racily clean entries	28,268 of 28,271	0
captureCheckpoint, 5 in a row	1,987–2,030 ms each	209–266 ms each
T3 local status (statusDetailsLocal)	3,734–3,774 ms each	83–127 ms each

On acerlinux, real T3 thread worktrees still had their creation-time index days later.

Change

GitVcsDriverCore.createWorktree now refreshes the new worktree's index once, after git worktree add and the submodule update, before it returns the worktree. Every T3 path that creates a worktree goes through this function: thread launch, PR worktree threads, the worktree MCP tool, checkpoint rollback, recreating a missing worktree at turn start, and the client's create-worktree request.

How it works:

1. It reads the index path with git rev-parse --git-path index and notes the index file's mtime second.
2. It runs git update-index -q --refresh --force-write-index.
   • -q exits 0 even when a file really is modified.
   • --force-write-index is needed for older Git: Git 2.30.9 leaves the index unwritten when racy entries merely check out clean. Git 2.53 writes either way.
3. If the rewritten index is still in the checkout's second, its entries are just as racy. In that case it waits until 50 ms past the end of that second and refreshes again; the margin covers file timestamps coming from a coarse kernel clock that can trail the wall clock. A 1,000-file checkout, for example, ends and refreshes within the same second. On t3code the first refresh takes about 1.3–1.8 s, so it never waits.
4. If that wait would be two seconds or more, the clock doesn't match the file timestamps (for example a network share stamped by another machine). It then skips the second refresh rather than guess. A virtual test clock also lands here, so existing tests don't wait.

Failure handling:

• Any failure is logged as a warning and ignored; the worktree is returned either way.
• The refresh gets the same 300 s timeout as git worktree add (WORKTREE_ADD_TIMEOUT_MS), since it re-reads every checked-out file and so scales with the checkout. Like worktree add, a timeout above the default keeps it out of the shared git process permits. When a timeout stops it, Git gets SIGTERM and removes its own index.lock. I checked this by killing a refresh 300 ms in: exit 143, no lock left, index unchanged.
• GIT_OPTIONAL_LOCKS=0, which the core driver sets for every command, doesn't stop update-index from writing (checked).

Why not run it in the background: a refresh holds index.lock for its whole run, which is 1.7 s on t3code. Thread launch starts the project setup script as soon as createWorktree returns, and agents may run git add or git checkout early. A background refresh would make those fail with "Unable to create index.lock: File exists", the failure #14718 removed from status polling. Running it before returning costs a one-time 1.3–1.8 s on t3code, or up to about 1 s on small repositories, when the worktree is created.

Scope and approval

Fixes #21328, which was accepted as a bug, and the triage named this exact gap: "a single missing refresh right after the worktree is created, before anything else uses it". It also endorsed the timing and safety constraints this change follows. The change is a one-time refresh in the one function that creates T3's worktrees. It doesn't change what gets checked out, how status or checkpoints work, or any setting.

It touches only GitVcsDriverCore.ts and its test. git merge-tree reports no conflict with #21315, #21329 or #21291.

A possible follow-up, not in this PR (the triage put clones out of scope for #21328): T3's project clone (git clone --progress in SourceControlRepositoryService) checks out sequentially, which leaves the files from its last second racily clean. A sequential checkout of t3code left 9,688 of 28,271 entries that way, and captures took 1.33 s instead of 0.21 s. The same refresh would apply there. Adding an existing folder as a project checks nothing out, so it isn't affected.

Verification

Tests, Git 2.53.0 and Node 26.12, on lenovolinux:

• cd apps/server && vp test run src/vcs/GitVcsDriverCore.test.ts: 167 passed. The 165 existing tests are unchanged; 2 are new.
  • "refreshes a new worktree's index once its checkout second is over" creates a 51-file worktree through the real driver, with the live clock, and asserts that no index entry is stamped in or after the index's own second.
  • "returns the worktree when its index refresh fails" uses a post-checkout hook to take the new worktree's index.lock. It asserts that createWorktree still returns a usable worktree, leaves that lock alone and logs the warning.
  • Run against origin/main's GitVcsDriverCore.ts, both fail in 5 of 5 runs. The first finds all 51 entries in the index's second; the second gets no warning, because nothing refreshes.
• All 12 server test files that create worktrees or touch checkpoints, including the three above: 844 passed.
  • cd apps/server && vp test run src/vcs/GitVcsDriverCore.test.ts src/vcs/GitVcsDriver.test.ts src/checkpointing/CheckpointStore.test.ts src/git/GitManager.test.ts src/mcp/toolkits/project/handlers.test.ts src/mcp/WorktreeMcpService.test.ts src/orchestration-v2/CheckpointRollbackService.test.ts src/orchestration-v2/ProviderEventIngestor.test.ts src/orchestration-v2/ProviderTurnStartService.test.ts src/orchestration-v2/runtimeLayer.test.ts src/orchestration-v2/ThreadLaunchService.test.ts src/storageCleanup.test.ts
  • Test time is essentially unchanged: the core suite took 19.5 s on main and 20.7 s here, including the new test's real wait of about 1 s. The other 9 files took 110.1 s against 110.3 s.
• Git 2.30.9, built from the kernel.org tarball, put first on PATH for the core suite:
  • main's driver: 159 passed, 8 failed. This branch: 161 passed, 6 failed.
  • The only differences are the two new tests. The other 6 failures are the same on both and come from Git 2.30 itself.
• cd apps/server && vp run --no-cache typecheck: no errors. vp lint and vp fmt --check on both files: nothing new. Two lint warnings elsewhere in these files predate this change.

Measured with a scratch test (not committed). It creates a worktree through the real GitVcsDriver.createWorktree with the live clock, then runs CheckpointStore.captureCheckpoint through the real VcsDriverRegistry and VcsProcess layers, with a small edit before each capture, and three statusDetailsLocal calls. Each round uses a fresh worktree.

t3code (28,271 files, from origin/main d8e9fd2). main had 6 rounds; this branch had 3 with the final code. How much of a fresh checkout is racy on main depends on where a second boundary falls during it: all of it in 3 rounds, 621–1,748 entries in the other 3.

	main, all racy (3)	main, partly racy (3)	this branch (3)
createWorktree	633–638 ms	628–659 ms	1,958–2,446 ms
Racily clean entries afterwards	28,268–28,271	621–1,748	0
First capture	2,063–3,693 ms	899–981 ms	242–253 ms
Next 5 captures	1,933–2,049 ms	449–576 ms	201–211 ms
T3 local status, 3 in a row	3,434–3,526 ms	585–745 ms	108–130 ms
createWorktree plus first capture	2.7–4.3 s	1.6 s	2.2–2.7 s

Three earlier branch rounds, alternated with three of the main rounds and run before I added --force-write-index (which changes nothing on Git 2.53), gave the same picture. createWorktree took 1,805–2,444 ms, captures 197–249 ms, and status 104–125 ms.

A 1,000-file repository (22 MB of t3code sources), 3 rounds on main and 6 on this branch (3 of them alternated with main and run before --force-write-index):

	main	this branch
createWorktree	71–73 ms (all 1,000 entries racy)	128–1,142 ms (0 racy)
First capture	148–232 ms	86–102 ms
Next 5 captures	118–208 ms	68–82 ms
T3 local status	112–132 ms	31–53 ms

So a small repository waits up to about 1 s once, to save about 50 ms per capture and about 80 ms per status refresh.

Not checked:

• macOS (the Mac was offline) and Windows.
• Network shares.
• Git versions other than 2.53.0 and 2.30.9; Git before 2.17 lacks --force-write-index, so there the refresh fails and is logged.
• A full thread launch through the app: I called createWorktree through the real driver layers, not through ThreadLaunchService and the UI.

Written by Claude Opus 5.5 in Claude Code, orchestrated from T3 Code.

[macroscopeapp]

Approvability

Verdict: Approved at 51ee6ff

Macroscope's review found this PR approvable — This is a focused bug fix that refreshes each newly created worktree index once, trading a bounded creation-time cost for eliminating repeated hashing during status and capture operations. It includes integration coverage for both successful refreshes and lock conflicts, without changing product defaults or static-analysis configuration.

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• apps/server/src/vcs/GitVcsDriverCore.ts

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📝 Walkthrough

New worktree creation now refreshes its Git index and may retry after the index timestamp boundary. Refresh failures produce a warning but do not prevent worktree creation. Tests cover index entry timestamps and a locked-index failure.

Changes: Worktree index refresh

Layer / File(s)	Summary
Refresh the new worktree index apps/server/src/vcs/GitVcsDriverCore.ts, apps/server/src/vcs/GitVcsDriverCore.test.ts	Adds a timestamp-based refresh for a new worktree index, including a conditional retry. A test checks that index entries are older than the index timestamp second.
Integrate refresh into worktree creation apps/server/src/vcs/GitVcsDriverCore.ts, apps/server/src/vcs/GitVcsDriverCore.test.ts	Worktree creation awaits the refresh and logs failures without failing creation. A test verifies this behavior when the index is locked.

Priority: ➖ Normal

Estimated code review effort: 3 (Moderate) | ~20 minutes

Change: Bug fix · Severity of issue fixed: Medium

Suggested reviewers: juliusmarminge

Merge Risk: ⚪ Minimal · up to 16028

New worktree creation now refreshes the Git index so later status and checkpoint calls are faster. Creation takes longer, by about 1.3 to 1.8 seconds in the author's trials. Refresh failures are logged and do not block creation. No merge-blocking risk is evident.

### Architecture Summary

Architecture risk: 🔵 Low · up to 16028

The change affects 1 system.

Changed systems: apps/server

Architecture concerns
No architecture-level concerns identified.

Review details

Systems and components

• observed — apps/server (service) was modified; 2 changed files map to changed impact.

Before / after behavior

• observed — Modified behavior in apps/server/src/vcs/GitVcsDriverCore.test.ts: Adds the Option import used by the new index timestamp test.
• observed — Modified behavior in apps/server/src/vcs/GitVcsDriverCore.test.ts: Adds a test that creates a worktree under a live clock, reads its index timestamp and entry mtimes, and asserts there are 51 entries and none is stamped in the index’s timestamp second or later.
• observed — Modified behavior in apps/server/src/vcs/GitVcsDriverCore.test.ts: Adds a test that locks the new worktree’s index from a checkout hook, then asserts creation returns the worktree and logs an index-refresh warning despite the lock.
• observed — Modified behavior in apps/server/src/vcs/GitVcsDriverCore.ts: Added the Clock import used to calculate the delay before a second index refresh.

Pre-merge checks: 4

Check name	Status	Explanation
Linked Issues check		Issue #21328 requires a one-time refresh after worktree creation and before use. The PR adds this in GitVcsDriverCore.createWorktree after checkout and submodule update. It uses `git update-index -q…
Out of Scope Changes check		The reported changes are limited to GitVcsDriverCore.ts and its test. The refresh, retry timing, failure handling, and tests directly support issue #21328. The PR does not add unrelated behavior or …
Title check		The title clearly and concisely describes the main change: refreshing indexes for new worktrees to prevent repeated file re-hashing. It uses a valid conventional commit format.
Description check		The description covers the problem, implementation, scope and approval, verification results, limitations, and agent attribution. It provides focused test commands and observed outcomes.

Full details: Linked Issues check

Explanation

Issue #21328 requires a one-time refresh after worktree creation and before use. The PR adds this in GitVcsDriverCore.createWorktree after checkout and submodule update. It uses git update-index -q --refresh --force-write-index, handles the timestamp boundary, logs failures, and still returns the worktree. The two added tests cover timestamp settling and refresh failure. The reported test results support the implementation. Project clones are not required for this worktree-specific fix.

Full details: Out of Scope Changes check

Explanation

The reported changes are limited to GitVcsDriverCore.ts and its test. The refresh, retry timing, failure handling, and tests directly support issue #21328. The PR does not add unrelated behavior or implement the separately identified clone follow-up.

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Actionable comments posted: 1

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• 🪄 Fix comments: Fix CodeRabbit comments on this PR

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Inline comments:
Review comments at @apps/server/src/vcs/GitVcsDriverCore.ts:
- Around line 3491-3496: Pass WORKTREE_ADD_TIMEOUT_MS to the runGit call for the
refresh operation in GitVcsDriver.createWorktree, so the index refresh uses the
checkout-sized timeout. Update the adjacent comment to identify this timeout.

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