fix(server): reuse Git index metadata during checkpoint capture

[im-kvijay]

What Changed

Checkpoint capture now seeds its private index from the workspace index and resets it to HEAD while retaining matching file metadata. The existing git add -A -- . then avoids rereading unchanged tracked files. The workspace index stays untouched.

Restore a conservative source-index timestamp after the reset, preserving Git's revalidation of racy entries even when read-tree rewrites the private index. Discard filesystem-monitor state during the reset. Fall back to the existing fresh-index path if copying or inspection fails, inspection is truncated, or assume-unchanged/skip-worktree flags remain.

Why

Starting with a fresh index throws away Git's stat cache on every capture. Reusing it reduces unnecessary work in large repositories while preserving scoped staging and snapshot contents.

Related to #3646; independent of the failed-write cleanup in #9809. Builds on the index-reuse approach explored in #8538, with a fresh-index fallback instead of normalizing special flags. Unlike #8301, this keeps native add -A staging rather than parsing changed paths. Discussion: #9808 (comment).

Validation

• 42 tests pass across GitVcsDriver, CheckpointStore, and VcsProcess; server typecheck, targeted lint, and formatting pass.
• The unchanged-file clean-filter regression fails on main and passes here. Tests cover two consecutive captures at root/nested directories, staged/unstaged/deleted/untracked files, special flags, split indexes, missing/corrupt indexes, same-size timestamp-preserving edits with core.trustctime=false (including fractional-second rounding and an edit after read-tree resets a two-file index), and an unchanged workspace index.
• Five paired complete captures on a 40,000-file fixture (10 modified, one untracked): median 244.1 ms → 71.6 ms (about 3.4× faster). Every paired snapshot tree matched and the workspace index remained byte-identical. Baseline: unoptimized driver at 4d06156dd. Rerun after correcting the timestamp restoration order.

The 30-second timeout is unchanged. Large new or modified files still need hashing; this does not claim to resolve every timeout in #3646.

Checklist

• This PR is small and focused
• I explained what changed and why

Implemented and verified with GPT-6 Astra through the Codex harness.

Summary by CodeRabbit

• Bug Fixes
  • Checkpoint capture now reliably detects same-size file edits, including edits with ambiguous timestamps.
  • Git index state is preserved more accurately during checkpoint capture, including staged changes, file metadata, and timestamps.
  • Improved handling of specially tracked files while retaining fallback behavior for invalid or unsupported index states.
  • Checkpoints continue to preserve deleted, newly added, and otherwise tracked file state.

[macroscopeapp]

Approvability

Verdict: Approved at e2e772f

Macroscope's review found this PR approvable — The change is a localized checkpoint-capture optimization with explicit fallback to the existing behavior and broad tests for Git index variants, filters, and scoped captures. It does not add a user-facing capability, alter schemas or defaults, or affect deployment, security, billing, or authentication.

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📝 Walkthrough

Walkthrough

captureCheckpoint now reuses a compatible Git index before creating a checkpoint. Tests cover clean-filter avoidance, racy timestamps, repeated captures, index modes, staged and special files, and missing or invalid indexes.

Changes

Checkpoint capture

Layer / File(s)	Summary
Working index reuse and fallback apps/server/src/vcs/GitVcsDriver.ts	captureCheckpoint copies and resets the working index when possible. It checks index flags and output status. It falls back to rebuilding the temporary index when reuse is invalid.
Checkpoint preservation tests apps/server/src/vcs/GitVcsDriver.test.ts	Tests verify clean-filter avoidance, racy timestamp handling, repeated captures, index-mode handling, preservation of staged and special files, and fallback for missing or invalid indexes.

Priority: ⬇️ Low

Estimated code review effort: 4 (Complex) | ~45 minutes

Merge Risk: ⚪ Minimal · up to 5d0af

The checkpoint index reuse changes are covered by passing regression tests and no unresolved merge risk remains.

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check. Docstring coverage is scoped to functions touched by this diff. Analyzed 0 functions across 2…
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Title check	✅ Passed	The title clearly and concisely describes the main change: reusing Git index metadata during checkpoint capture.
Description check	✅ Passed	The description includes the required What Changed, Why, and Checklist sections. It also provides detailed validation results. UI sections are not required because this change does not affect the UI.

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[TheCrazyLex]

This fixed the persistent timeout issue I have and issue #3646 - @t3dotgg @maria-rcks please check if this fix can be merged please

[shivamhwp]

Note: GPT-6 on behalf of shivam (@shivamhwp).

Copying the index gives it a new modification time and can defeat Git's racy-index protection. With core.trustctime=false, an indexed file whose timestamp equals the original index timestamp can be edited to different same-length content while retaining that timestamp. The original index is still racy, but the fresh copy appears newer than the file. read-tree --reset HEAD preserves its cached metadata and add -A skips the edit, so the checkpoint contains the old bytes.

Preserve a conservative source-index timestamp on the private copy before asking Git to reuse its metadata, or otherwise force revalidation of entries that were racy against the source index. Keep the user index untouched. Add coverage for a same-size timestamp-preserving edit with core.trustctime=false, alongside the existing unchanged-file filter case.

[im-kvijay]

@shivamhwp Confirmed and fixed in 8679610. The private copy now receives an earlier whole-second timestamp derived from the source index before read-tree --reset HEAD. This retains Git's racy-entry revalidation and accounts for Date rounding fractional milliseconds upward. The correction adds six production lines.

Added same-size, timestamp-preserving edits with core.trustctime=false, at both an exact second and a fractional-second boundary. Both capture the old bytes on the previous PR version and the new bytes with this fix. They verify the workspace index's bytes and mtime stay unchanged. The existing unchanged-file clean-filter test still passes.

All 40 focused tests, the server typecheck, targeted lint, and formatting pass. The paired 40,000-file benchmark still shows a median 245.4 ms → 77.0 ms (about 3.2× faster), with identical trees. Updated the PR description with the correction and fresh measurements.

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Inline comments:
In `@apps/server/src/vcs/GitVcsDriver.ts`:
- Line 750: In captureCheckpoint, move the fileSystem.utimes call for
tempIndexPath to after the read-tree --reset HEAD operation so the timestamp
remains valid. Add a two-file regression test that stages one file, runs the
reset, applies a same-size timestamp-preserving edit to the other file, and
verifies git add -A -- . stages the updated content.

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[im-kvijay]

(gpt 6 astra) Checked current main (6fd68f5c3): checkpoint capture still initializes a fresh index, so an equivalent index-reuse fix has not landed. #8301 remains open; #8538 closed without merging.

Merged main in c75c3f7. Resolved the test-file insertion conflict by retaining both our capture regressions and the new empty-checkpoint restore test from #11338. Upstream's restore implementation is preserved; our capture optimization and timestamp fixes are unchanged.

All 42 focused Git/checkpoint tests, the server typecheck, targeted lint, formatting, and diff checks pass. The diff against current main remains limited to the original two files.