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fix(server): new worktrees refresh their index once, so captures and status stop re-hashing every file - #21341
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 (https://git.cafe/pingdotgg/t3code/issues/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:
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:
It reads the index path with git rev-parse --git-path index and notes the index file's mtime second.
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.
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.
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 https://git.cafe/pingdotgg/t3code/pulls/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 https://git.cafe/pingdotgg/t3code/issues/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.
A possible follow-up, not in this PR (the triage put clones out of scope for https://git.cafe/pingdotgg/t3code/issues/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:
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/maind8e9fd2). 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.
…ach status and checkpoint
`git worktree add` stamps most files in the second it writes the index,
and Git re-reads every file stamped in the index's own second or later.
Nothing T3 runs ever rewrites a worktree's index (status polling uses
GIT_OPTIONAL_LOCKS=0 and captures work on a copy), so in a new t3code
worktree every capture took about 2 s and every status refresh 3.5 s,
until the agent or user happened to run an index-writing git command
(pingdotgg#21328).
createWorktree now runs `git update-index -q --refresh
--force-write-index` once in the new worktree before returning it; Git
2.30 otherwise skips the write. If that refresh finishes within the
checkout's second, it waits the second out and refreshes again. Failures
are logged and ignored. It runs before the worktree is returned because a
refresh holds index.lock, which a background run would race against the
setup script and the agent.
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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Walkthrough
New worktree creation refreshes its Git index after submodule setup. The refresh checks index timestamps and may retry after the checkout’s timestamp second. Refresh failures produce a warning and do not prevent worktree creation. Tests cover index entry timestamps and a locked index.
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 index entry timestamps against 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.
New worktree creation now refreshes the Git index once so later status and checkpoint operations are faster. Refresh failures are logged and do not block creation. No merge-blocking risk is evident.
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
Title check
The title clearly and concisely describes the main change: refreshing new worktree indexes to prevent repeated file re-hashing. It uses a conventional commit format and is specific to the changeset.
Description check
The description includes all required sections: Problem, Change, Scope and approval, and Verification. It explains the issue, implementation, scope, linked issue, test results, performance measurement…
Linked Issues check
Issue #21328 requires new worktrees to stop retaining racily clean index entries. GitVcsDriverCore.createWorktree now calls refreshNewWorktreeIndex after checkout and submodule setup, before retur…
Out of Scope Changes check
The whole-PR diff changes only GitVcsDriverCore.ts and its test. Production changes implement the index refresh, timeout, clock guard, retry, and failure handling required for issue #21328. Test cha…
Full details: Description check
Explanation
The description includes all required sections: Problem, Change, Scope and approval, and Verification. It explains the issue, implementation, scope, linked issue, test results, performance measurements, and untested environments in sufficient detail.
Full details: Linked Issues check
Explanation
Issue #21328 requires new worktrees to stop retaining racily clean index entries. GitVcsDriverCore.createWorktree now calls refreshNewWorktreeIndex after checkout and submodule setup, before return. The helper runs git update-index -q --refresh --force-write-index, waits past the index timestamp second when required, and retries unless the clock delay is unsafe. It uses the five-minute refresh timeout. It logs failures and still returns the worktree. The added tests cover timestamp cleanup and a locked-index failure. The clone follow-up remains outside this issue's approved scope.
Full details: Out of Scope Changes check
Explanation
The whole-PR diff changes only GitVcsDriverCore.ts and its test. Production changes implement the index refresh, timeout, clock guard, retry, and failure handling required for issue #21328. Test changes validate that behavior. No capture, status, checkpoint, checkout-content, settings, or clone behavior changes appear in the diff.
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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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Merged current main without rebasing at f52c67ae3db169deebc93f09435f1028900697e1. Resolved both conflicts by preserving main's early branch-base resolution and locale hook test alongside the contributor's index refresh and its two tests. The refresh still has its dedicated five-minute timeout. The diff remains two files, 146 added lines.
Blacksmith vp run check:changed github/main passed format, lint, knip, generated GraphQL checks, three affected-package typechecks, and all 236 tests. Two independent reviews found no issues on this head.
Runtime verification on this head: started a real Codex gpt-6-luna turn through thread start --worktree fix/worktree-index-refresh; it completed and read the package name correctly. Read-only index inspection found 0 racy entries out of 29,219 and no index.lock. Playwright with /usr/bin/google-chrome opened the resulting thread in the client and confirmed the completed reply, worktree branch, and clean +0/-0 changes. This is an index-state check, not a performance measurement.
Native desktop/mobile, other operating systems, network shares, other Git versions, and the five-minute deadline were not exercised in this pass. Previous before/after provider/client evidence remains in the separate verification comment.
Verified head 9fcaae4801ca1ec7adccc8dfe0d6a7bc24c6f30c as-is on Linux with Git 2.43.0, repository Playwright 1.60.0 and /usr/bin/google-chrome. Ran one dev server at a time, with fresh isolated app state and no mocks or seeded data.
On github/main (955e2bfbb5), added the real repository through the web client, selected New worktree from github/main, and submitted a real Codex gpt-6.1-sol turn that read package.json and created a one-line file. After the turn and checkpoint, 27,054 of 29,069 index entries remained in or after the index's mtime second. Repeated the same client flow, checkout and prompt on the PR: 0 of 29,069 racy entries, with no index.lock remaining. The index inspection used read-only Git commands with GIT_OPTIONAL_LOCKS=0.
Both versions completed the provider turn and persisted ready initial/post-turn checkpoints. On the PR, a second Codex turn appended a line and successfully ran git add; its staged diff contained both lines. The third checkpoint was ready. Reloading the client preserved the conversation, cumulative +2 change, and latest-turn diff showing the second line. No code changes were needed. This verifies the index state through actual thread launch; it is not a latency benchmark.
Blacksmith: vp i && cd apps/server && vp test run src/vcs/GitVcsDriverCore.test.ts passed all 214 tests, including timestamp settling and locked-index fallback. CI reports 29 successful checks.
Native desktop, iOS/Android, macOS/Windows, network shares, other Git versions, submodule worktrees, and the five-minute timeout were not exercised in this Linux app pass. Refresh failure under a held index lock was covered by the existing real-Git test, not manually induced through the UI. Other providers and remote/tunnel connections were not exercised.
On Linux with Git 2.43.0, ran each commit's real server and web client with fresh isolated state, the same 12,001-file synthetic repository, fast checkout disabled, a 1280×800 viewport, and light theme. Created new worktree threads and completed two small edits/checkpoints using a deterministic ACP fixture agent that runs no Git commands. Inspected the index and repeated status reads from each thread terminal with optional index writes disabled.
AI-assisted; verified with the tests and tools listed above.
Not shown:
End-to-end Changes refresh and checkpoint durations were not instrumented; the recordings show completed edits/checkpoints, while terminal diagnostics directly demonstrate repeated unchanged file reads.
The initial worktree creation delay, refresh failure fallback, older Git versions, and other operating systems were not measured.
The scenario runner was not used because its documentation explicitly excludes performance regressions based on replay timing.
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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 (https://git.cafe/pingdotgg/t3code/issues/21328).
git worktree addwrites the files first and the index last. Git re-reads, on every status, diff andadd, each file whose mtime falls in the index's own second or later. With thecheckout.workers=0thatcreateWorktreepasses, 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:GIT_OPTIONAL_LOCKS=0and plumbingdiff-index(https://git.cafe/pingdotgg/t3code/pulls/14718);--no-optional-locks, and Codex's startup left the index unwritten too.Numbers from https://git.cafe/pingdotgg/t3code/issues/21328, measured in such a worktree:
git update-index -q --refreshcaptureCheckpoint, 5 in a rowstatusDetailsLocal)On acerlinux, real T3 thread worktrees still had their creation-time index days later.
Change
GitVcsDriverCore.createWorktreenow refreshes the new worktree's index once, aftergit worktree addand 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:
git rev-parse --git-path indexand notes the index file's mtime second.git update-index -q --refresh --force-write-index.-qexits 0 even when a file really is modified.--force-write-indexis 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.Failure handling:
git worktree add(WORKTREE_ADD_TIMEOUT_MS), since it re-reads every checked-out file and so scales with the checkout. Likeworktree 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 ownindex.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 stopupdate-indexfrom writing (checked).Why not run it in the background: a refresh holds
index.lockfor its whole run, which is 1.7 s on t3code. Thread launch starts the project setup script as soon ascreateWorktreereturns, and agents may rungit addorgit checkoutearly. A background refresh would make those fail with "Unable to create index.lock: File exists", the failure https://git.cafe/pingdotgg/t3code/pulls/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 https://git.cafe/pingdotgg/t3code/issues/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.tsand its test.git merge-treereports no conflict with https://git.cafe/pingdotgg/t3code/pulls/21315, https://git.cafe/pingdotgg/t3code/pulls/21329 or https://git.cafe/pingdotgg/t3code/pulls/21291.A possible follow-up, not in this PR (the triage put clones out of scope for https://git.cafe/pingdotgg/t3code/issues/21328): T3's project clone (
git clone --progressinSourceControlRepositoryService) 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.post-checkouthook to take the new worktree'sindex.lock. It asserts thatcreateWorktreestill returns a usable worktree, leaves that lock alone and logs the warning.origin/main'sGitVcsDriverCore.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.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.tsmainand 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.PATHfor the core suite:main's driver: 159 passed, 8 failed. This branch: 161 passed, 6 failed.cd apps/server && vp run --no-cache typecheck: no errors.vp lintandvp fmt --checkon 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.createWorktreewith the live clock, then runsCheckpointStore.captureCheckpointthrough the realVcsDriverRegistryandVcsProcesslayers, with a small edit before each capture, and threestatusDetailsLocalcalls. Each round uses a fresh worktree.t3code (28,271 files, from
origin/maind8e9fd2).mainhad 6 rounds; this branch had 3 with the final code. How much of a fresh checkout is racy onmaindepends 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)createWorktreecreateWorktreeplus first captureThree earlier branch rounds, alternated with three of the
mainrounds and run before I added--force-write-index(which changes nothing on Git 2.53), gave the same picture.createWorktreetook 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
mainand 6 on this branch (3 of them alternated withmainand run before--force-write-index):maincreateWorktreeSo 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:
--force-write-index, so there the refresh fails and is logged.createWorktreethrough the real driver layers, not throughThreadLaunchServiceand the UI.Written by Claude Opus 5.5 in Claude Code, orchestrated from T3 Code.
Fixes #21328