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Fix: Normalize FilesTouched paths to prevent missing checkpoint trail… #779

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Fix: Normalize FilesTouched paths to prevent missing checkpoint trail… #779

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17 changes: 15 additions & 2 deletions cmd/entire/cli/strategy/content_overlap.go
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Original file line number Diff line number Diff line change
Expand Up @@ -186,10 +186,14 @@ func filesOverlapWithContent(ctx context.Context, repo *git.Repository, shadowBr
func stagedFilesOverlapWithContent(ctx context.Context, repo *git.Repository, shadowTree *object.Tree, stagedFiles, filesTouched []string) bool {
logCtx := logging.WithComponent(ctx, "checkpoint")

// Build set of filesTouched for quick lookup
// Build set of filesTouched for quick lookup.
// Normalize to base filenames as a fallback to handle path format mismatches
// (absolute vs repo-relative) from stale sessions or older CLI versions (#768).
touchedSet := make(map[string]bool)
touchedByBase := make(map[string]bool) // fallback: basename-only lookup
for _, f := range filesTouched {
touchedSet[f] = true
touchedByBase[filepath.Base(f)] = true
}

// Get HEAD tree to determine if files are being modified or newly created
Expand Down Expand Up @@ -232,8 +236,17 @@ func stagedFilesOverlapWithContent(ctx context.Context, repo *git.Repository, sh

// Check each staged file
for _, stagedPath := range stagedFiles {
// Try exact path match first, then fall back to basename match.
// This handles stale sessions or older CLI versions that stored
// absolute paths in FilesTouched (#768).
if !touchedSet[stagedPath] {
continue // Not in filesTouched, skip
if !touchedByBase[filepath.Base(stagedPath)] {
continue // Not in filesTouched by exact or basename, skip
}
logging.Debug(logCtx, "stagedFilesOverlapWithContent: path format mismatch, matched by basename",
slog.String("staged_path", stagedPath),
slog.Any("files_touched", filesTouched),
)
}

// Check if this is a modified file (exists in HEAD) or new file
Expand Down
26 changes: 21 additions & 5 deletions cmd/entire/cli/strategy/manual_commit_git.go
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Original file line number Diff line number Diff line change
Expand Up @@ -141,7 +141,8 @@ func (s *ManualCommitStrategy) SaveStep(ctx context.Context, step StepContext) e
state.PromptAttributions = append(state.PromptAttributions, promptAttr)

// Track touched files (modified, new, and deleted)
state.FilesTouched = mergeFilesTouched(state.FilesTouched, step.ModifiedFiles, step.NewFiles, step.DeletedFiles)
// Normalize paths to repo-relative form to prevent path format mismatches (#768)
state.FilesTouched = mergeFilesTouched(state.WorktreePath, state.FilesTouched, step.ModifiedFiles, step.NewFiles, step.DeletedFiles)

// On first checkpoint, record the transcript identifier for this session
if state.StepCount == 1 {
Expand Down Expand Up @@ -273,7 +274,8 @@ func (s *ManualCommitStrategy) SaveTaskStep(ctx context.Context, step TaskStepCo
}

// Track touched files (modified, new, and deleted)
state.FilesTouched = mergeFilesTouched(state.FilesTouched, step.ModifiedFiles, step.NewFiles, step.DeletedFiles)
// Normalize paths to repo-relative form to prevent path format mismatches (#768)
state.FilesTouched = mergeFilesTouched(state.WorktreePath, state.FilesTouched, step.ModifiedFiles, step.NewFiles, step.DeletedFiles)

// Save updated state
if err := s.saveSessionState(ctx, state); err != nil {
Expand Down Expand Up @@ -315,15 +317,17 @@ func (s *ManualCommitStrategy) SaveTaskStep(ctx context.Context, step TaskStepCo
}

// mergeFilesTouched merges multiple file lists into existing touched files, deduplicating.
func mergeFilesTouched(existing []string, fileLists ...[]string) []string {
// All paths are normalized to repo-relative form using worktreePath to prevent
// path format mismatches between absolute agent paths and repo-relative git paths (#768).
func mergeFilesTouched(worktreePath string, existing []string, fileLists ...[]string) []string {
seen := make(map[string]bool)
for _, f := range existing {
seen[f] = true
seen[normalizeToRepoRelative(f, worktreePath)] = true
}

for _, list := range fileLists {
for _, f := range list {
seen[f] = true
seen[normalizeToRepoRelative(f, worktreePath)] = true
}
}

Expand All @@ -337,6 +341,18 @@ func mergeFilesTouched(existing []string, fileLists ...[]string) []string {
return result
}

// normalizeToRepoRelative converts a file path to repo-relative form.
// If the path is already relative or worktreePath is empty, the path is returned as-is.
func normalizeToRepoRelative(filePath, worktreePath string) string {
if worktreePath == "" || !filepath.IsAbs(filePath) {
return filePath
}
if rel := paths.ToRelativePath(filePath, worktreePath); rel != "" {
return rel
}
return filePath
}

// accumulateTokenUsage adds new token usage to existing accumulated usage.
// If existing is nil, returns a copy of incoming. If incoming is nil, returns existing unchanged.
func accumulateTokenUsage(existing, incoming *agent.TokenUsage) *agent.TokenUsage {
Expand Down