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.

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

• 38 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, and an unchanged workspace index.
• Five paired complete captures on a 40,000-file fixture (10 modified, one untracked): median 242.5 ms → 74.1 ms (about 3.3× faster). Every paired snapshot tree matched and the workspace index remained byte-identical. Baseline: 061543e9e.

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 preserves existing file state more reliably, including staged, deleted, newly added, and specially tracked files.
  • Improved handling of missing or invalid Git index states, with graceful fallback behavior.
  • Avoided unnecessary filter processing for unchanged indexed files during checkpoint capture.
  • Checkpoint reuse now better preserves the original index across different repository configurations.

[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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[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: Path: .coderabbit.yaml

Review profile: CHILL

Plan: Advanced

Run ID: 5e7309d2-1a06-4578-950f-230dc6f63c64

📥 Commits

Reviewing files that changed from the base of the PR and between 061543e and e2e772f.

📒 Files selected for processing (2)

• apps/server/src/vcs/GitVcsDriver.test.ts
• apps/server/src/vcs/GitVcsDriver.ts

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📝 Walkthrough

Walkthrough

captureCheckpoint now reuses compatible Git index state before creating a checkpoint. Tests cover unchanged-file filters, repeated captures, index modes, staged work, 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 falls back to rebuilding the temporary index when flags, truncation, or index errors prevent reuse.
Checkpoint preservation tests apps/server/src/vcs/GitVcsDriver.test.ts	Tests verify filter avoidance, repeated checkpoint capture, index-mode handling, preservation of staged and special files, and fallback for missing or invalid indexes.

Priority: ➖ Normal — Schedule the Git checkpoint performance change because it reduces capture time in large repositories while preserving snapshot contents and workspace index state.

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

Merge Risk: ⚪ Minimal · up to e2e77

Checkpoint capture should become faster while preserving snapshot contents and the workspace index; the supplied validation shows no actionable merge-blocking risk.

Suggested reviewers: t3dotgg

🚥 Pre-merge checks | ✅ 5

✅ Passed checks (5 passed)

Check name	Status	Explanation
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 explains the fallback behavior, validation results, performance impact, and confirms that the workspace index remain…
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.

✨ Finishing Touches

🧪 Generate unit tests (beta)

• Create PR with unit tests

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