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fix(checkpoints): keep files ignored at checkpoint time on restore - #1840
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restoreCheckpoint ran `git clean -f -d -f` against the workspace's current ignore rules. Files ignored when a checkpoint was saved were never committed to it, so after .gitignore changed (for example, an agent overwrote it) they were no longer ignored and the clean deleted them. Each checkpoint now records the paths ignored when it was saved (`git ls-files --others --ignored --exclude-standard --directory`). Restore removes only untracked files ignored by neither the current rules nor that record, then prunes directories left empty, as `git clean -d` did. Checkpoints saved before this change have no record and keep the previous clean. Fixes Zoo-Code-Org#1832 Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
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📝 SummarySummary by CodeRabbit
WalkthroughCheckpoint creation now records ignored workspace paths. Restore uses that record to preserve paths ignored at checkpoint time while removing other untracked paths. Checkpoints without a record retain the previous cleanup behavior. ChangesCheckpoint restore behavior
Priority: ➖ Normal Estimated code review effort: 3 (Moderate) | ~20 minutes Change: Bug fix · Severity of issue fixed: Medium Merge Risk: 🔵 Low · up to Restore now preserves files that were ignored when a checkpoint was saved. Two edge cases remain. If rewriting an ignore record fails partway, a later restore can lose protection for those files. Restore also leaves empty folders created after the checkpoint. Both fixes are small and localized. Making the record write atomic is advisable before merge. Security Architecture ReviewSecurity architecture risk: 🟡 Moderate · up to The change addresses a real data-loss case, but a failed or interrupted metadata write can leave a new checkpoint unable to protect the files it was meant to preserve. Repeated saves can also expand which files survive a later restore. Retained concerns
Security review detailsSecurity Blast Radius
Security Findings and Attack Paths
Trust Boundaries and Controls
Resilience and Maintainability Implications
Hardening Proposals
Caution Pre-merge checks failedPlease resolve all errors before merging. Addressing warnings is optional.
❌ Failed checks (2 errors, 1 warning)
✅ Passed checks (5 passed)
Full details: Regression EvidenceExplanation The new restore tests cover checkpoint-time ignored paths, changed Resolution Add focused integration tests in Full details: Security BoundariesExplanation The changed path trusts an unvalidated restore hash as a filesystem path. Resolution Validate Full details: Persistence IntegrityExplanation The changed sidecar persistence path is not integrity-safe. Resolution Write each ignored-path record to a temporary file in the same directory, flush it as required, and atomically rename it over the old record. Preserve the previous valid record when the update fails. Do not treat arbitrary read errors as a missing record; distinguish ✨ Finishing Touches🧪 Generate unit tests (beta)
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Actionable comments posted: 4
- 🪄 Fix CodeRabbit comments on this PR
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Inline comments:
Review comments at
@src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts:
- Around line 350-352: Update the ignore-rule tests around saveCheckpoint in
ShadowCheckpointService.spec.ts, including the test starting at line 324, to use
an untracked secret path and assert before saving that the shadow Git index does
not track it and git check-ignore reports it as ignored. Include a positive
control confirming the ignore rule matches, using behavior-focused assertions.
- Around line 369-383: Update the legacy-checkpoint test around `saveCheckpoint`
and `restoreCheckpoint` to distinguish the fallback cleanup path: create a path
ignored when the checkpoint is saved, change its ignore rule, remove the ignore
record, then assert that restoration produces the expected legacy `git.clean`
result for that path.
Review comments at @src/services/checkpoints/ShadowCheckpointService.ts:
- Around line 316-318: Update the `git.raw` `ls-files` invocation in the restore
flow to include directory entries with `--directory`, so empty untracked
directories are considered for cleanup. Preserve the existing safeguards that
prevent deleting directories containing preserved files.
- Line 297: Update the ignored-record write in ShadowCheckpointService to write
the serialized paths to a temporary file and rename it to the path returned by
ignoredRecordPath only after the write succeeds, preserving the existing record
if writing fails.
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src/services/checkpoints/ShadowCheckpointService.tssrc/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts
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Check persistence and lifecycle invariants: awaited atomic writes, rollback or explicit partial-failure behavior, cross-window state consistency, stale listeners/watchers, cancellation, idempotency, and safe restart/resume without lost or d...
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Files:
src/services/checkpoints/__tests__/ShadowCheckpointService.spec.tssrc/services/checkpoints/ShadowCheckpointService.ts
Require regression coverage at the lowest valid harness with behavior-focused assertions, including relevant negative, error, false/unset, and boundary cases.
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Files:
src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts
Check strict typing and exhaustive behavior across normal, boundary, error, cancellation, retry, and compatibility paths.
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Files:
src/services/checkpoints/__tests__/ShadowCheckpointService.spec.tssrc/services/checkpoints/ShadowCheckpointService.ts
Verify extension/webview contracts, cancellation and error propagation, VS Code lifecycle correctness, and behavior under retries and partial failure.
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src/services/checkpoints/__tests__/ShadowCheckpointService.spec.tssrc/services/checkpoints/ShadowCheckpointService.ts
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src/services/checkpoints/__tests__/ShadowCheckpointService.spec.tssrc/services/checkpoints/ShadowCheckpointService.ts
🪛 ast-grep (0.45.3)
src/services/checkpoints/__tests__/ShadowCheckpointService.spec.ts
[warning] 327-327: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(gitignore, ".gitignore\nsecrets/\n")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 329-329: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(secret, "untracked and ignored")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 333-333: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(gitignore, "dist/\n")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 335-335: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(createdAfter, "new")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 339-339: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.readFile(secret, "utf-8")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 341-341: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.readFile(gitignore, "utf-8")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 348-348: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(gitignore, "secrets/\n")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 350-350: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(secret, "untracked and ignored")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 354-354: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(gitignore, "dist/\n")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 357-357: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(createdAfter, "new")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 361-361: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.readFile(secret, "utf-8")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 363-363: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.readFile(gitignore, "utf-8")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 369-369: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(testFile, "checkpointed")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 377-377: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(createdAfter, "new")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 381-381: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.readFile(testFile, "utf-8")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
src/services/checkpoints/ShadowCheckpointService.ts
[warning] 281-281: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.readFile(this.ignoredRecordPath(commitHash), "utf8")
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
[warning] 296-296: Filesystem path is not a string literal; a request-/variable-derived path can enable path traversal. Validate and normalize the path before use.
Context: fs.writeFile(this.ignoredRecordPath(commitHash), [...ignored].join("\0"))
Note: [CWE-22] Improper Limitation of a Pathname to a Restricted Directory ('Path Traversal').
(detect-non-literal-fs-filename-typescript)
🪛 GitHub Check: mutation-diff
src/services/checkpoints/ShadowCheckpointService.ts
[warning] 335-335: Mutation test advisory
src/services/checkpoints/ShadowCheckpointService.ts:335: 4 mutation test gaps; example: NoCoverage ConditionalExpression mutant (replacement: true). See the job summary for the complete list and resolution guidance.
[warning] 334-334: Mutation test advisory
src/services/checkpoints/ShadowCheckpointService.ts:334: 9 mutation test gaps; example: NoCoverage ConditionalExpression mutant (replacement: true). See the job summary for the complete list and resolution guidance.
[warning] 328-328: Mutation test advisory
src/services/checkpoints/ShadowCheckpointService.ts:328: NoCoverage ArithmeticOperator mutant (replacement: b.length + a.length). See the job summary for the complete list and resolution guidance.
[warning] 323-323: Mutation test advisory
src/services/checkpoints/ShadowCheckpointService.ts:323: 2 mutation test gaps; example: Survived BooleanLiteral mutant (replacement: false). See the job summary for the complete list and resolution guidance.
[warning] 311-311: Mutation test advisory
src/services/checkpoints/ShadowCheckpointService.ts:311: Survived StringLiteral mutant (replacement: ""). See the job summary for the complete list and resolution guidance.
[warning] 300-300: Mutation test advisory
src/services/checkpoints/ShadowCheckpointService.ts:300: NoCoverage StringLiteral mutant (replacement: ``). See the job summary for the complete list and resolution guidance.
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Amp-Thread-ID: https://ampcode.com/threads/T-01a10cc3-928d-7028-bd4b-83dcc6816f1b Co-authored-by: Amp <amp@ampcode.com>
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Related GitHub Issue
Closes: #1832
Description
restoreCheckpointrangit clean -f -d -fbeforegit reset --hard, and the shadow repo's worktree is the workspace, so the clean applied the workspace's current ignore rules. Files that were ignored when the checkpoint was saved were never committed to it. If.gitignorechanged afterwards (in the issue, an agent overwrote it withwrite_to_file), those files were no longer ignored and the clean deleted them. This also happens when.gitignoreitself is in the checkpoint, because the clean runs before the reset restores it.This PR follows the issue's second suggestion: a file is kept if it is ignored under either the checkpoint-time rules or the current rules.
initShadowGitandsaveCheckpoint), the paths ignored at that moment are recorded withgit ls-files --others --ignored --exclude-standard --directory. Fully ignored directories such asnode_modules/collapse to one entry. The record is stored per commit at<shadow .git>/zoo-checkpoint-ignored/<hash>. Repeated saves of the same hash add to the record rather than replace it. A recording failure is logged and never fails the save.git ls-files --others --exclude-standard(current rules), and any path covered by the checkpoint's record is skipped. The rest are removed, and directories left empty are pruned, asgit clean -ddid. Nested repositories listed asdir/are removed recursively, as the previous-f -fdid.git clean -f -d -fbehaviour.Not included: the issue's first point, making
write_to_filerefuse to overwrite existing files. That changes the tool's intended behaviour rather than fixing a defect, so it's left for maintainers to decide separately.Test Procedure
New tests in
ShadowCheckpointService.spec.ts(real git repositories in temp directories):.gitignorelists itself andsecrets/, a checkpoint is saved, then.gitignoreis overwritten. After restore,secrets/key.txtis kept, the never-checkpointed.gitignoreis kept as-is, and a file created after the checkpoint is removed..gitignorethat changes:secrets/key.txtis kept,.gitignoreis restored, and a file created after the checkpoint is removed together with its new directory.The first two tests fail on
main(ENOENTforsecrets/key.txt, i.e. the file was deleted).cd src npx vitest run services/checkpoints core/checkpointsResults: all checkpoint suites passed; type checking and ESLint passed (also via the commit hook). ESLint suppression counts are unchanged.
Pre-Submission Checklist
Visual Snapshots
Not applicable; no UI changes.
Videos (interaction / animation only)
Not applicable.
Documentation Updates
Additional Notes
Cost: one extra
git ls-filescall per checkpoint save, which walks the same treegit addalready does, with ignored directories collapsed.🤖 Generated with Claude Code