[saphid]

Problem

Reverting files to a checkpoint can leave files behind if the agent created a new .gitignore during the turns being undone. For example, the agent scaffolds web/, writes web/.gitignore with node_modules/, dist/ and .env, then runs npm install. After "Revert files too", web/node_modules/… and web/.env are still on disk.

The cause is that restore runs git clean -fd once. That pass deletes the new .gitignore files, but Git read them during the same scan, so it skipped the files they ignored. Once the .gitignore is gone, those files are no longer ignored. They show up as untracked (?? web/), and the next turn's checkpoint stages them with git add -A, so node_modules ends up in checkpoint objects and diffs.

Change

restoreCheckpoint repeats git clean -fd while the previous pass removed something (at most four passes). It recreates the workspace before each pass, as the existing single pass does. A restore that cleans nothing still runs one pass. Files that stay ignored under the restored rules are still kept, as before.

If the fourth pass still removed something (a chain of more than four nested .gitignore files the turn created), restore runs git clean -dn. If that still lists paths, restore fails with the same git clean error as other clean failures, instead of reporting success with files left behind.

Scope and approval

Very small, focused fix for an obvious bug, so no prior issue: restore promises to put the workspace back to the checkpoint, and here it leaves files the agent created that are not ignored. The fix is about 20 lines in one function, and one existing test case gains about 14 lines.

Overlap search: local PR index and REST search for restore/revert/rollback/gitignore/clean. Open restore PRs #28647 (unborn branch staging), #23671 (restore vs. new turns), #21809 (stale/replay guards) and #16863 (restore order) do not touch the git clean step.

Verification

• Red on main: extended restores empty checkpoints without changing paths outside the workspace in GitVcsDriver.test.ts with an untracked untracked/.gitignore hiding untracked/hidden.txt. It fails with AssertionError: expected true to be false at assert.isFalse(exists(cwd/untracked)). The same case also builds a chain of five nested .gitignore files and expects restore to fail. Before the pass-limit check, that restore returned true (Unknown Error: true from Effect.flip).
• Green: vp test run src/vcs/GitVcsDriver.test.ts src/checkpointing/CheckpointStore.test.ts -> 76 passed. After rebasing on current main, vp test run src/vcs/GitVcsDriver.test.ts -> 67 passed. With the pass-limit check: vp test run src/vcs/GitVcsDriver.test.ts src/checkpointing/CheckpointStore.test.ts -> 76 passed.
• vp run check:changed: format, lint, knip, typecheck (3 packages) and tests all pass.
• Real git transcript (same commands as the driver): before the fix, git status --short after restore showed ?? debug.log and ?? web/ (web/.env, web/node_modules/pkg/index.js). A second git clean -fd printed Removing debug.log and Removing web/, and a third printed nothing.
• Not checked: Windows. The loop recreates the workspace before every pass, which covers the existing case where Windows removes ./ and exits 0.

Reviewed with sol-loop: 2 rounds with GPT-6.1 Sol on high (one for the fix, one for the pass-limit check). Sol verdict: approved.

Created with Claude Opus 5.5 in Claude Code (T3 Code).

🤖 Generated with Claude Code

[macroscopeapp]

Approvability

Verdict: Needs Human Approval

Macroscope's review found this PR requires human approval — Repeated cleanup fixes leftovers after reverting newly created .gitignore files, but also permanently deletes newly exposed untracked files, potentially including local .env contents. Human confirmation is needed that this broader deletion matches the intended revert contract, since checkpoints may not contain those files.

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

[coderabbitai]

No actionable comments were generated in the recent review.

Walkthrough

Checkpoint restoration retries cleanup when Git reports removed paths. It checks for remaining untracked files after retries and resets the index when cleanup fails. Tests cover nested ignore rules, cleanup failure, and nested repository restoration.

Changes: Checkpoint restoration

Layer / File(s)	Summary
Restore cleanup and index state apps/server/src/vcs/GitVcsDriver.ts, apps/server/src/vcs/GitVcsDriver.test.ts	Restore uses a shared index-reset helper and retries cleanup up to three times when Git reports removals. A dry run checks for remaining untracked files; remaining files cause an index reset and cleanup failure. Other cleanup failures also reset the index. Tests cover nested ignore rules, restore failure state, and nested repository restoration.

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

Change: Bug fix

Suggested reviewers: josephv123

Merge Risk: Minimal · up to e13f1

No actionable restore defect remains identified; the change is mergeable after normal checks.

Pre-merge checks: 4

Check name	Status	Explanation
Title check		The title names the main change: restoring files now removes untracked files that a new .gitignore from the turn had been hiding. It uses a conventional commit prefix and matches the restoreCheckpoint…
Description check		The description follows the template sections (Problem, Change, Scope and approval, Verification). The Problem section gives the cause and a reproduction example. The Change section explains the bound…
Linked Issues check		Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check		Check skipped because no linked issues were found for this pull request.

Full details: Title check

Explanation

The title names the main change: restoring files now removes untracked files that a new .gitignore from the turn had been hiding. It uses a conventional commit prefix and matches the restoreCheckpoint and git clean changes in GitVcsDriver.ts and its test.

Full details: Description check

Explanation

The description follows the template sections (Problem, Change, Scope and approval, Verification). The Problem section gives the cause and a reproduction example. The Change section explains the bounded clean loop, the workspace recreation, and the dry-run failure path. Scope gives a small-fix justification with an overlap search. Verification gives red and green test results, a real git transcript, and notes what was not checked (Windows). The template's HTML comment blocks are left in place. The description does not include an approval link, but it explains why the fix qualifies as a small, focused bug fix without a prior issue, as the template allows.

Finishing Touches

Generate unit tests (beta)

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Recent review info

Run configuration

• Source mode: Auto
• Repository: pingdotgg/t3code
• Branch: main
• File: .coderabbit.config.ts
• Commit: 0a86e15
• Layers: Repository TS config
• Review profile: CHILL
• Plan: Advanced
• Run ID: 34834367-832c-461e-9fe4-7c6f52db5767

Commits

Reviewing files that changed from the base of the PR and between e7ac911 and e13f1b5.

Files selected for processing: 2

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

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[coderabbitai]

• Fix comments: Fix CodeRabbit comments on this PR

[saphid]

Note

🤖 Claude Opus 5.5 responding on behalf of saphid

On Macroscope's concern about .env and other local files: I ran the restore steps with real git (git 2.50.1). The checkpoint used a temporary index from HEAD plus git add -A, like captureCheckpoint. Then restore ran git restore --source <cp> --worktree --staged -- ., repeated git clean -fd -- ., and git reset. In the setup, .gitignore ignores secrets.env. The turn creates web/.gitignore (node_modules/, .env), web/.env and web/node_modules/…, and edits the root .env.

File	Before the turn	main (one pass)	This PR
.env (untracked, not ignored, existed before the turn)	in the checkpoint	restored to its contents before the turn	restored to its contents before the turn
secrets.env (ignored by an existing rule)	not in the checkpoint	untouched	untouched
web/.env (created during the turn, hidden by the turn's web/.gitignore)	did not exist	left behind, shows as ?? web/	removed
web/.env (existed before the turn, later hidden by the turn's web/.gitignore)	in the checkpoint	restored	restored; only web/node_modules/ is removed

Revert contract: a file that existed before the turn and was not ignored is in the checkpoint, so restore brings it back. A file ignored by rules in the checkpoint is never touched. Only files created after the checkpoint that are not ignored by the checkpoint's rules are removed. main already removes those files when no new .gitignore hides them. This PR applies the same rule to files a turn's new .gitignore was hiding. A file the user created during the turn under such a .gitignore is removed too, exactly like an unhidden untracked file on main.

A maintainer should confirm this is the intended revert behavior.

[coderabbitai]

• Fix comments: Fix CodeRabbit comments on this PR

[maria-rcks]

Note

Written by gpt-6.1-sol on behalf of Maria

Verified in a real dev environment

verified on linux with /usr/bin/google-chrome, repo playwright, the running dev web client, and real codex gpt-6.1-sol turns. projects, isolated worktrees, files, and checkpoints were created through the app and provider. no mocks or seeded scenarios.

• reproduced on github/main (61c3794c32): after "edit from here" → "revert files too", web/.gitignore disappeared but web/.env and web/node_modules/pkg/index.js remained as untracked files.
• the original pr head removed those files, but a protected untracked nested git repository made restore fail with "untracked files remain". fixed on the existing branch in e7ac91124693daeb4e2f26fd9785ed7c554c3b21: count git removal lines, preserve informational skip lines, and reset the workspace index before returning cleanup errors.
• restarted and rechecked the corrected head: the generated web/ directory was removed; tracked files returned to baseline; the pre-existing ignored secret and nested repository survived. "revert and keep changes" preserved the edited file.
• exercised the four-pass limit through another real codex thread. captured the running server's cleanup error with an empty staged diff and restored checkpoint contents. the effect worker then retried and completed cleanup.
• blacksmith: 76 focused vcs/checkpoint tests passed. vp run check:changed d8a829e5ecd6626f8fdee23ef20ca9758e056251 passed format, lint, knip, graphql, affected typechecks, and 68 tests. the two extended regression assertions failed before the correction.

command transcript with filesystem and server evidence

the recording shows the actual rewind interaction. the transcript proves disk cleanup independently of the changes counter. uploaded playback and seeking were checked.

github strips the external video player here. the inspected recording is shared in the verification thread; this screenshot shows the reproduced nested-repository failure before the correction.

Not verified

native ios/android and electron clients, windows/macOS filesystem behavior, and other providers were not exercised on this linux vm. this pass exercised the shared server restore through the web client and codex.

[saphid]

Note

🤖 Claude Opus 5.5 responding on behalf of saphid

Merged main (e13f1b5) to resolve a conflict in restoreCheckpoint. #28647 made the final git reset --quiet -- . unconditional, so reverting before the first commit no longer leaves files staged. This branch had moved that reset into the resetIndex helper, which every cleanup-failure path calls, behind a hasHeadCommit check. The merge keeps the helper and drops that check, so the success path and every failure path follow #28647. GitVcsDriver.test.ts passes 71/71, including #28647's before-first-commit case and this PR's nested-repository, pass-limit and index-reset cases.