fix(server): stage only changed checkpoint paths

[PetrSeifert]

What Changed

• Discover checkpoint paths with a scoped, NUL-delimited git status using the real index.
• Stage only those paths into the temporary checkpoint index through --pathspec-from-file.
• Preserve raw Git pathname bytes from status -z output through pathspec stdin, including non-UTF-8 names.
• Preserve workspace-subdirectory scope and leave the user's real index unchanged.
• Fall back to the existing scoped full add only if status output exceeds the preview limit.
• Add focused unit and Git integration coverage for staged, unstaged, deleted, and untracked paths.

Why

Checkpoint capture currently builds a temporary index with git add -A -- .. On repositories with hundreds of thousands of tracked files, that can exceed the 30-second process timeout even when only a few files changed. The missing checkpoint then prevents Latest turn diffs and summaries from loading.

This change keeps the checkpoint content equivalent while limiting temporary-index staging to the paths Git already reports as changed.

Related to #3646. This PR targets large repositories with a small changed-file set. It does not claim to add failure backoff, temporary-pack cleanup, or handling for a single oversized untracked file.

Testing

• vp test run apps/server/src/stream/collectUint8StreamText.test.ts apps/server/src/processRunner.test.ts apps/server/src/vcs/VcsProcess.test.ts apps/server/src/vcs/GitVcsDriver.test.ts
• vp lint --report-unused-disable-directives apps/server/src/vcs/GitVcsDriver.ts apps/server/src/vcs/GitVcsDriver.test.ts
• vp run --filter t3 typecheck
• git diff --check upstream/main...HEAD

Checklist

• This PR is small and focused
• I explained what changed and why
• No UI changes

---

Note

Medium Risk
Changes core checkpoint staging and relies on porcelain v1 byte parsing; a format mismatch could miss paths until the slower add -A fallback runs.

Overview
Checkpoint capture no longer runs git add -A -- . on the temporary index for every capture. It runs a scoped, NUL-delimited git status --porcelain=v1 -z (with GIT_OPTIONAL_LOCKS=0), parses changed paths from the raw status bytes, and stages only those paths via git add --literal-pathspecs … --pathspec-from-file=- from the repository root. Repositories without HEAD seed the temp index with read-tree --empty. If status output is truncated or raw bytes are missing, behavior falls back to the previous scoped git add -A -- ..

Process I/O gains optional binary-safe plumbing: stdin can be Uint8Array, captureStdoutBytes returns stdoutBytes alongside decoded text (with stdoutInvalidUtf8), wired through VcsProcess, processRunner, and collectUint8StreamText so NUL-delimited git output and pathspec stdin stay lossless.

New unit and integration tests cover raw byte round-trips, exact git commands for checkpoint staging (including invalid-UTF-8 paths), and that scoped checkpoints match the working tree without mutating the real index.

^{Reviewed by Cursor Bugbot for commit 0f8cb9a. Bugbot is set up for automated code reviews on this repo. Configure here.}

Note

Fix captureCheckpoint to stage only changed paths via binary-safe pathspecs

• Reworks captureCheckpoint in GitVcsDriver.ts to run git status --porcelain=v1 -z with captureStdoutBytes, parse the raw bytes into a NUL-delimited pathspec, and feed it to git add --pathspec-from-file=- --pathspec-file-nul against a temp index — so only changed paths are staged instead of git add -A
• Adds parseCheckpointStatusPathspec to extract NUL-terminated paths from porcelain status bytes, handling files with spaces or invalid UTF-8
• Propagates Uint8Array stdin and captureStdoutBytes through VcsProcess and ProcessRunner so raw bytes flow end-to-end without UTF-8 corruption
• Uses resolveRepositoryRoot to run the pathspec-based git add at the repo root so paths resolve correctly
• Risk: captureCheckpoint falls back to git add -A -- . in the scoped cwd when status output is truncated or raw bytes are unavailable; reviewers should confirm the fallback in GitVcsDriver.captureCheckpoint preserves prior behavior under large diffs

^{Macroscope summarized 0f8cb9a.}

[coderabbitai]

Important

Review skipped

Auto reviews are disabled on this repository. Please check the settings in the CodeRabbit UI or the .coderabbit.yaml file in this repository. To trigger a single review, invoke the @coderabbitai review command.

⚙️ Run configuration

Configuration used: Repository UI

Review profile: CHILL

Plan: Pro Plus

Run ID: 1a5acaa5-e0f5-4859-b150-fde492bd681d

You can disable this status message by setting the reviews.review_status to false in the CodeRabbit configuration file.

Use the checkbox below for a quick retry:

• 🔍 Trigger review

---

_{Comment @coderabbitai help to get the list of available commands.}

[cursor]

Cursor Bugbot has reviewed your changes using high effort and found 1 potential issue.

^{❌ Bugbot Autofix is OFF. To automatically fix reported issues with cloud agents, enable autofix in the Cursor dashboard.}

Want fixes drafted automatically? Bugbot Autofix can create code changes for findings. A team admin can enable Autofix in the Cursor dashboard.

^{Reviewed by Cursor Bugbot for commit 585a2f8. Configure here.}

[macroscopeapp]

Approvability

Verdict: Not approved

Macroscope's review found this PR not approvable — This production bug fix changes the checkpoint-capture pipeline for every Git workspace, replacing full staging with autonomous status-based path selection and adding shared binary process plumbing. The behavior is well tested, but the runtime gate and cross-cutting implementation create enough staging and correctness risk to warrant human review.

^{You can add or adjust custom eligibility rules. Learn more.}