fix: Prevent bd sync from committing non-.beads files (bd-trgb)

gitCommit() was adding the JSONL file but then committing ALL staged
changes (no pathspec). If other files were staged (e.g., deletions from
git add -A), they would be swept into the bd sync commit.

Fixed by adding pathspec to both gitCommit() and commitToExternalBeadsRepo()
so they only commit what they explicitly staged.

This was the root cause of PR #722 files being deleted - they were staged
for deletion in the working tree and got committed by bd sync.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com>

cmd/bd/sync.go

@@ -893,7 +893,9 @@ func gitCommit(ctx context.Context, filePath string, message string) error {
 	}
 
 	// Commit from repo root context with config-based author and signing options
-	commitArgs := buildGitCommitArgs(repoRoot, message)
+	// Use pathspec to commit ONLY this file (bd-trgb fix)
+	// This prevents accidentally committing other staged files
+	commitArgs := buildGitCommitArgs(repoRoot, message, "--", relPath)
 	commitCmd := exec.CommandContext(ctx, "git", commitArgs...)
 	output, err := commitCmd.CombinedOutput()
 	if err != nil {

cmd/bd/sync_branch.go

@@ -240,10 +240,12 @@ func commitToExternalBeadsRepo(ctx context.Context, beadsDir, message string, pu
 	}
 
 	// Commit with config-based author and signing options
+	// Use pathspec to commit ONLY beads files (bd-trgb fix)
+	// This prevents accidentally committing other staged files
 	if message == "" {
 		message = fmt.Sprintf("bd sync: %s", time.Now().Format("2006-01-02 15:04:05"))
 	}
-	commitArgs := buildGitCommitArgs(repoRoot, message)
+	commitArgs := buildGitCommitArgs(repoRoot, message, "--", relBeadsDir)
 	commitCmd := exec.CommandContext(ctx, "git", commitArgs...) //nolint:gosec // args from buildGitCommitArgs
 	if output, err := commitCmd.CombinedOutput(); err != nil {
 		return false, fmt.Errorf("git commit failed: %w\n%s", err, output)