chore: code health review - test fix and error comments (bd-9g1z, bd-ork0)

- Remove TestFindJSONLPathDefault from .test-skip (now passes)
- Add explanatory comments to 24 ignored error locations in cmd/bd:
  - Cobra flag methods (MarkHidden, MarkRequired, MarkDeprecated)
  - Best-effort cleanup/close operations
  - Process signaling operations

Part of code health review epic bd-tggf.

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

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

.test-skip

@@ -1,5 +1,4 @@
 # Tests to skip due to known issues
 # Format: one test name per line (regex patterns supported)
 
-# Issue #356: Expects wrong JSONL filename (issues.jsonl vs beads.jsonl)
-TestFindJSONLPathDefault
+# (no tests currently skipped)

cmd/bd/create.go

@@ -399,7 +399,7 @@ func init() {
 	registerCommonIssueFlags(createCmd)
 	createCmd.Flags().StringSliceP("labels", "l", []string{}, "Labels (comma-separated)")
 	createCmd.Flags().StringSlice("label", []string{}, "Alias for --labels")
-	_ = createCmd.Flags().MarkHidden("label")
+	_ = createCmd.Flags().MarkHidden("label") // Only fails if flag missing (caught in tests)
 	createCmd.Flags().String("id", "", "Explicit issue ID (e.g., 'bd-42' for partitioning)")
 	createCmd.Flags().String("parent", "", "Parent issue ID for hierarchical child (e.g., 'bd-a3f8e9')")
 	createCmd.Flags().StringSlice("deps", []string{}, "Dependencies in format 'type:id' or 'id' (e.g., 'discovered-from:bd-20,blocks:bd-15' or 'bd-20')")

cmd/bd/daemon_autostart.go

@@ -224,7 +224,7 @@ func acquireStartLock(lockPath, socketPath string) bool {
 	}
 
 	_, _ = fmt.Fprintf(lockFile, "%d\n", os.Getpid())
-	_ = lockFile.Close()
+	_ = lockFile.Close() // Best-effort close during startup
 	return true
 }
 
@@ -257,9 +257,9 @@ func handleExistingSocket(socketPath string) bool {
 	}
 
 	debugLog("socket is stale, cleaning up")
-	_ = os.Remove(socketPath)
+	_ = os.Remove(socketPath) // Best-effort cleanup, file may not exist
 	if pidFile != "" {
-		_ = os.Remove(pidFile)
+		_ = os.Remove(pidFile) // Best-effort cleanup, file may not exist
 	}
 	return false
 }
@@ -353,7 +353,7 @@ func canDialSocket(socketPath string, timeout time.Duration) bool {
 	if err != nil || client == nil {
 		return false
 	}
-	_ = client.Close()
+	_ = client.Close() // Best-effort close after health check
 	return true
 }
 

cmd/bd/daemon_lifecycle.go

@@ -303,7 +303,7 @@ func stopDaemon(pidFile string) {
 	}
 	
 	// Clean up stale artifacts after forced kill
-	_ = os.Remove(pidFile)
+	_ = os.Remove(pidFile) // Best-effort cleanup, file may not exist
 	
 	// Also remove socket file if it exists
 	if _, err := os.Stat(socketPath); err == nil {

cmd/bd/daemon_lock.go

@@ -70,16 +70,16 @@ func acquireDaemonLock(beadsDir string, dbPath string) (*DaemonLock, error) {
 		StartedAt: time.Now().UTC(),
 	}
 	
-	_ = f.Truncate(0)
+	_ = f.Truncate(0)              // Clear file for fresh write (we hold lock)
 	_, _ = f.Seek(0, 0)
 	encoder := json.NewEncoder(f)
 	encoder.SetIndent("", "  ")
-	_ = encoder.Encode(lockInfo)
-	_ = f.Sync()
+	_ = encoder.Encode(lockInfo)   // Write can't fail if Truncate succeeded
+	_ = f.Sync()                   // Best-effort sync to disk
 
 	// Also write PID file for Windows compatibility (can't read locked files on Windows)
 	pidFile := filepath.Join(beadsDir, "daemon.pid")
-	_ = os.WriteFile(pidFile, []byte(fmt.Sprintf("%d\n", os.Getpid())), 0600)
+	_ = os.WriteFile(pidFile, []byte(fmt.Sprintf("%d\n", os.Getpid())), 0600) // Best-effort PID write
 
 	return &DaemonLock{file: f, path: lockPath}, nil
 }

cmd/bd/duplicate.go

@@ -49,11 +49,11 @@ var (
 
 func init() {
 	duplicateCmd.Flags().StringVar(&duplicateOf, "of", "", "Canonical issue ID (required)")
-	_ = duplicateCmd.MarkFlagRequired("of")
+	_ = duplicateCmd.MarkFlagRequired("of") // Only fails if flag missing (caught in tests)
 	rootCmd.AddCommand(duplicateCmd)
 
 	supersedeCmd.Flags().StringVar(&supersededWith, "with", "", "Replacement issue ID (required)")
-	_ = supersedeCmd.MarkFlagRequired("with")
+	_ = supersedeCmd.MarkFlagRequired("with") // Only fails if flag missing (caught in tests)
 	rootCmd.AddCommand(supersedeCmd)
 }
 

cmd/bd/migrate.go

@@ -721,9 +721,9 @@ func cleanupWALFiles(dbPath string) {
 	walPath := dbPath + "-wal"
 	shmPath := dbPath + "-shm"
 	
-	// Best effort - don't fail if these don't exist
-	_ = os.Remove(walPath)
-	_ = os.Remove(shmPath)
+	// Best effort cleanup - don't fail if these don't exist
+	_ = os.Remove(walPath) // WAL may not exist
+	_ = os.Remove(shmPath) // SHM may not exist
 }
 
 // handleInspect shows migration plan and database state for AI agent analysis

cmd/bd/migrate_issues.go

@@ -708,6 +708,6 @@ func init() {
 	migrateIssuesCmd.Flags().Bool("strict", false, "Fail on orphaned dependencies or missing repos")
 	migrateIssuesCmd.Flags().Bool("yes", false, "Skip confirmation prompt")
 
-	_ = migrateIssuesCmd.MarkFlagRequired("from")
-	_ = migrateIssuesCmd.MarkFlagRequired("to")
+	_ = migrateIssuesCmd.MarkFlagRequired("from") // Only fails if flag missing (caught in tests)
+	_ = migrateIssuesCmd.MarkFlagRequired("to")   // Only fails if flag missing (caught in tests)
 }

cmd/bd/mol_spawn.go

@@ -256,7 +256,7 @@ func init() {
 	molSpawnCmd.Flags().String("attach-type", types.BondTypeSequential, "Bond type for attachments: sequential, parallel, or conditional")
 	molSpawnCmd.Flags().Bool("pour", false, "Create persistent mol in .beads/ (default: wisp in .beads-wisp/)")
 	molSpawnCmd.Flags().Bool("persistent", false, "Deprecated: use --pour instead")
-	_ = molSpawnCmd.Flags().MarkDeprecated("persistent", "use --pour instead")
+	_ = molSpawnCmd.Flags().MarkDeprecated("persistent", "use --pour instead") // Only fails if flag missing
 
 	molCmd.AddCommand(molSpawnCmd)
 }

cmd/bd/reset.go

@@ -322,7 +322,7 @@ func stopDaemonQuiet(pidFile string) {
 		return
 	}
 
-	_ = sendStopSignal(process)
+	_ = sendStopSignal(process) // Best-effort graceful stop
 
 	// Wait for daemon to stop gracefully
 	for i := 0; i < daemonShutdownAttempts; i++ {
@@ -333,7 +333,7 @@ func stopDaemonQuiet(pidFile string) {
 	}
 
 	// Force kill if still running
-	_ = process.Kill()
+	_ = process.Kill() // Best-effort force kill, process may have already exited
 }
 
 func removeGitattributesEntry() error {

cmd/bd/show.go

@@ -1394,7 +1394,7 @@ func init() {
 	registerCommonIssueFlags(updateCmd)
 	updateCmd.Flags().String("notes", "", "Additional notes")
 	updateCmd.Flags().String("acceptance-criteria", "", "DEPRECATED: use --acceptance")
-	_ = updateCmd.Flags().MarkHidden("acceptance-criteria")
+	_ = updateCmd.Flags().MarkHidden("acceptance-criteria") // Only fails if flag missing (caught in tests)
 	updateCmd.Flags().IntP("estimate", "e", 0, "Time estimate in minutes (e.g., 60 for 1 hour)")
 	updateCmd.Flags().StringSlice("add-label", nil, "Add labels (repeatable)")
 	updateCmd.Flags().StringSlice("remove-label", nil, "Remove labels (repeatable)")

cmd/bd/snapshot_manager.go

@@ -192,6 +192,7 @@ func (sm *SnapshotManager) Cleanup() error {
 	basePath, leftPath := sm.getSnapshotPaths()
 	baseMetaPath, leftMetaPath := sm.getSnapshotMetadataPaths()
 
+	// Best-effort cleanup of snapshot files (may not exist)
 	_ = os.Remove(basePath)
 	_ = os.Remove(leftPath)
 	_ = os.Remove(baseMetaPath)

cmd/bd/sync.go

@@ -1402,7 +1402,7 @@ func exportToJSONL(ctx context.Context, jsonlPath string) error {
 		exportedIDs = append(exportedIDs, issue.ID)
 	}
 
-	// Close temp file before rename
+	// Close temp file before rename (error checked implicitly by Rename success)
 	_ = tempFile.Close()
 
 	// Atomic replace

cmd/bd/tips.go

@@ -154,7 +154,7 @@ func getLastShown(store storage.Storage, tipID string) time.Time {
 func recordTipShown(store storage.Storage, tipID string) {
 	key := fmt.Sprintf("tip_%s_last_shown", tipID)
 	value := time.Now().Format(time.RFC3339)
-	_ = store.SetMetadata(context.Background(), key, value)
+	_ = store.SetMetadata(context.Background(), key, value) // Non-critical metadata, ok to fail silently
 }
 
 // InjectTip adds a dynamic tip to the registry at runtime.

docs/TESTING.md

@@ -67,11 +67,6 @@ Tests in `.test-skip` are automatically skipped. Current broken tests:
    - Issue: Database deadlock, hangs for 5 minutes
    - Impact: Makes test suite extremely slow
 
-2. **TestFindJSONLPathDefault** (GH #356)
-   - Location: `internal/beads/beads_test.go:175`
-   - Issue: Expects `issues.jsonl` but code returns `beads.jsonl`
-   - Impact: Assertion failure
-
 ## For Claude Code / AI Agents
 
 When running tests during development: