feat(doctor): add patrol pollution detection and fix

Add CheckPatrolPollution to detect stale patrol beads:
- Patrol digests matching 'Digest: mol-*-patrol'
- Session ended beads matching 'Session ended: *'

Includes auto-fix via 'bd doctor --fix' to clean up pollution.

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

cmd/bd/doctor.go

@@ -612,9 +612,10 @@ func runDiagnostics(path string) doctorResult {
 	result.Checks = append(result.Checks, staleMQFilesCheck)
 	// Don't fail overall check for legacy MQ files, just warn
 
-	// Note: Check 26d (misclassified wisps) was referenced but never implemented.
+	// Check 26d: Patrol pollution (patrol digests, session beads)
-	// The commit f703237c added importer-based auto-detection instead.
+	patrolPollutionCheck := convertDoctorCheck(doctor.CheckPatrolPollution(path))
-	// Removing the undefined reference to fix build.
+	result.Checks = append(result.Checks, patrolPollutionCheck)
+	// Don't fail overall check for patrol pollution, just warn
 
 	// Check 27: Expired tombstones (maintenance)
 	tombstonesExpiredCheck := convertDoctorCheck(doctor.CheckExpiredTombstones(path))

cmd/bd/doctor/fix/maintenance.go

@@ -6,6 +6,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"strings"
 	"time"
 
 	"github.com/steveyegge/beads/internal/beads"
@@ -173,3 +174,100 @@ func ExpiredTombstones(path string) error {
 	fmt.Printf("  Pruned %d expired tombstone(s) (older than %d days)\n", prunedCount, ttlDays)
 	return nil
 }
+
+// PatrolPollution deletes patrol digest and session ended beads that pollute the database.
+// This is the fix handler for the "Patrol Pollution" doctor check.
+//
+// It removes beads matching:
+// - Patrol digests: titles matching "Digest: mol-*-patrol"
+// - Session ended beads: titles matching "Session ended: *"
+//
+// After deletion, runs compact --purge-tombstones equivalent to clean up.
+func PatrolPollution(path string) error {
+	if err := validateBeadsWorkspace(path); err != nil {
+		return err
+	}
+
+	beadsDir := filepath.Join(path, ".beads")
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+
+	if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
+		fmt.Println("  No JSONL file found, nothing to clean up")
+		return nil
+	}
+
+	// Get database path
+	var dbPath string
+	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
+		dbPath = cfg.DatabasePath(beadsDir)
+	} else {
+		dbPath = filepath.Join(beadsDir, beads.CanonicalDatabaseName)
+	}
+
+	ctx := context.Background()
+	store, err := sqlite.New(ctx, dbPath)
+	if err != nil {
+		return fmt.Errorf("failed to open database: %w", err)
+	}
+	defer func() { _ = store.Close() }()
+
+	// Get all issues and identify pollution
+	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
+	if err != nil {
+		return fmt.Errorf("failed to query issues: %w", err)
+	}
+
+	var patrolDigestCount, sessionBeadCount int
+	var toDelete []string
+
+	for _, issue := range issues {
+		// Skip tombstones
+		if issue.DeletedAt != nil {
+			continue
+		}
+
+		title := issue.Title
+
+		// Check for patrol digest pattern: "Digest: mol-*-patrol"
+		if strings.HasPrefix(title, "Digest: mol-") && strings.HasSuffix(title, "-patrol") {
+			patrolDigestCount++
+			toDelete = append(toDelete, issue.ID)
+			continue
+		}
+
+		// Check for session ended pattern: "Session ended: *"
+		if strings.HasPrefix(title, "Session ended:") {
+			sessionBeadCount++
+			toDelete = append(toDelete, issue.ID)
+		}
+	}
+
+	if len(toDelete) == 0 {
+		fmt.Println("  No patrol pollution beads to delete")
+		return nil
+	}
+
+	// Delete all pollution beads
+	var deleted int
+	for _, id := range toDelete {
+		if err := store.DeleteIssue(ctx, id); err != nil {
+			fmt.Printf("  Warning: failed to delete %s: %v\n", id, err)
+			continue
+		}
+		deleted++
+	}
+
+	// Report results
+	if patrolDigestCount > 0 {
+		fmt.Printf("  Deleted %d patrol digest bead(s)\n", patrolDigestCount)
+	}
+	if sessionBeadCount > 0 {
+		fmt.Printf("  Deleted %d session ended bead(s)\n", sessionBeadCount)
+	}
+	fmt.Printf("  Total: %d pollution bead(s) removed\n", deleted)
+
+	// Suggest running compact to purge tombstones
+	fmt.Println("  💡 Run 'bd compact --purge-tombstones' to reclaim space")
+
+	return nil
+}

cmd/bd/doctor/maintenance.go

@@ -520,3 +520,172 @@ func CheckMisclassifiedWisps(path string) DoctorCheck {
 		Category: CategoryMaintenance,
 	}
 }
+
+// PatrolPollutionThresholds defines when to warn about patrol pollution
+const (
+	PatrolDigestThreshold = 10 // Warn if patrol digests > 10
+	SessionBeadThreshold  = 50 // Warn if session beads > 50
+)
+
+// PatrolPollutionResult contains counts of detected pollution beads
+type PatrolPollutionResult struct {
+	PatrolDigestCount int      // Count of "Digest: mol-*-patrol" beads
+	SessionBeadCount  int      // Count of "Session ended: *" beads
+	PatrolDigestIDs   []string // Sample IDs for display
+	SessionBeadIDs    []string // Sample IDs for display
+}
+
+// CheckPatrolPollution detects patrol digest and session ended beads that pollute the database.
+// These beads are created during patrol operations and should not persist in the database.
+//
+// Patterns detected:
+// - Patrol digests: titles matching "Digest: mol-*-patrol"
+// - Session ended beads: titles matching "Session ended: *"
+func CheckPatrolPollution(path string) DoctorCheck {
+	beadsDir := resolveBeadsDir(filepath.Join(path, ".beads"))
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+
+	if _, err := os.Stat(jsonlPath); os.IsNotExist(err) {
+		return DoctorCheck{
+			Name:     "Patrol Pollution",
+			Status:   StatusOK,
+			Message:  "N/A (no JSONL file)",
+			Category: CategoryMaintenance,
+		}
+	}
+
+	// Read JSONL and count pollution beads
+	file, err := os.Open(jsonlPath) // #nosec G304 - path constructed safely
+	if err != nil {
+		return DoctorCheck{
+			Name:     "Patrol Pollution",
+			Status:   StatusOK,
+			Message:  "N/A (unable to read JSONL)",
+			Category: CategoryMaintenance,
+		}
+	}
+	defer file.Close()
+
+	result := detectPatrolPollution(file)
+
+	// Check thresholds
+	hasPatrolPollution := result.PatrolDigestCount > PatrolDigestThreshold
+	hasSessionPollution := result.SessionBeadCount > SessionBeadThreshold
+
+	if !hasPatrolPollution && !hasSessionPollution {
+		return DoctorCheck{
+			Name:     "Patrol Pollution",
+			Status:   StatusOK,
+			Message:  "No patrol pollution detected",
+			Category: CategoryMaintenance,
+		}
+	}
+
+	// Build warning message
+	var warnings []string
+	if hasPatrolPollution {
+		warnings = append(warnings, fmt.Sprintf("%d patrol digest beads (should be 0)", result.PatrolDigestCount))
+	}
+	if hasSessionPollution {
+		warnings = append(warnings, fmt.Sprintf("%d session ended beads (should be wisps)", result.SessionBeadCount))
+	}
+
+	// Build detail with sample IDs
+	var details []string
+	if len(result.PatrolDigestIDs) > 0 {
+		details = append(details, fmt.Sprintf("Patrol digests: %v", result.PatrolDigestIDs))
+	}
+	if len(result.SessionBeadIDs) > 0 {
+		details = append(details, fmt.Sprintf("Session beads: %v", result.SessionBeadIDs))
+	}
+
+	return DoctorCheck{
+		Name:     "Patrol Pollution",
+		Status:   StatusWarning,
+		Message:  strings.Join(warnings, ", "),
+		Detail:   strings.Join(details, "; "),
+		Fix:      "Run 'bd doctor --fix' to clean up patrol pollution",
+		Category: CategoryMaintenance,
+	}
+}
+
+// detectPatrolPollution scans a JSONL file for patrol pollution patterns
+func detectPatrolPollution(file *os.File) PatrolPollutionResult {
+	var result PatrolPollutionResult
+	decoder := json.NewDecoder(file)
+
+	for {
+		var issue types.Issue
+		if err := decoder.Decode(&issue); err != nil {
+			break
+		}
+
+		// Skip tombstones
+		if issue.DeletedAt != nil {
+			continue
+		}
+
+		title := issue.Title
+
+		// Check for patrol digest pattern: "Digest: mol-*-patrol"
+		if strings.HasPrefix(title, "Digest: mol-") && strings.HasSuffix(title, "-patrol") {
+			result.PatrolDigestCount++
+			if len(result.PatrolDigestIDs) < 3 {
+				result.PatrolDigestIDs = append(result.PatrolDigestIDs, issue.ID)
+			}
+			continue
+		}
+
+		// Check for session ended pattern: "Session ended: *"
+		if strings.HasPrefix(title, "Session ended:") {
+			result.SessionBeadCount++
+			if len(result.SessionBeadIDs) < 3 {
+				result.SessionBeadIDs = append(result.SessionBeadIDs, issue.ID)
+			}
+		}
+	}
+
+	return result
+}
+
+// GetPatrolPollutionIDs returns all IDs of patrol pollution beads for deletion
+func GetPatrolPollutionIDs(path string) ([]string, error) {
+	beadsDir := resolveBeadsDir(filepath.Join(path, ".beads"))
+	jsonlPath := filepath.Join(beadsDir, "issues.jsonl")
+
+	file, err := os.Open(jsonlPath) // #nosec G304 - path constructed safely
+	if err != nil {
+		return nil, fmt.Errorf("failed to open issues.jsonl: %w", err)
+	}
+	defer file.Close()
+
+	var ids []string
+	decoder := json.NewDecoder(file)
+
+	for {
+		var issue types.Issue
+		if err := decoder.Decode(&issue); err != nil {
+			break
+		}
+
+		// Skip tombstones
+		if issue.DeletedAt != nil {
+			continue
+		}
+
+		title := issue.Title
+
+		// Check for patrol digest pattern
+		if strings.HasPrefix(title, "Digest: mol-") && strings.HasSuffix(title, "-patrol") {
+			ids = append(ids, issue.ID)
+			continue
+		}
+
+		// Check for session ended pattern
+		if strings.HasPrefix(title, "Session ended:") {
+			ids = append(ids, issue.ID)
+		}
+	}
+
+	return ids, nil
+}

cmd/bd/doctor_fix.go

@@ -312,6 +312,8 @@ func applyFixList(path string, fixes []doctorCheck) {
 			continue
 		case "Legacy MQ Files":
 			err = doctor.FixStaleMQFiles(path)
+		case "Patrol Pollution":
+			err = fix.PatrolPollution(path)
 		default:
 			fmt.Printf("  ⚠ No automatic fix available for %s\n", check.Name)
 			fmt.Printf("  Manual fix: %s\n", check.Fix)