Merge origin/main

cmd/bd/daemon.go

@@ -179,6 +179,19 @@ func init() {
 	daemonCmd.Flags().BoolVar(&jsonOutput, "json", false, "Output JSON format")
 	rootCmd.AddCommand(daemonCmd)
 }
+
+// computeDaemonParentPID determines which parent PID the daemon should track.
+// When BD_DAEMON_FOREGROUND=1 (used by startDaemon for background CLI launches),
+// we return 0 to disable parent tracking, since the short-lived launcher
+// process is expected to exit immediately after spawning the daemon.
+// In all other cases we track the current OS parent PID.
+func computeDaemonParentPID() int {
+	if os.Getenv("BD_DAEMON_FOREGROUND") == "1" {
+		// 0 means "not tracked" in checkParentProcessAlive
+		return 0
+	}
+	return os.Getppid()
+}
 func runDaemonLoop(interval time.Duration, autoCommit, autoPush bool, logPath, pidFile string, global bool) {
 	logF, log := setupDaemonLogger(logPath)
 	defer func() { _ = logF.Close() }()
@@ -422,7 +435,7 @@ func runDaemonLoop(interval time.Duration, autoCommit, autoPush bool, logPath, p
 	doSync()
 
 	// Get parent PID for monitoring (exit if parent dies)
-	parentPID := os.Getppid()
+	parentPID := computeDaemonParentPID()
 	log.log("Monitoring parent process (PID %d)", parentPID)
 
 	// Choose event loop based on BEADS_DAEMON_MODE

cmd/bd/daemon_watcher.go

@@ -6,6 +6,7 @@ import (
 	"os"
 	"path/filepath"
 	"strings"
+	"sync"
 	"time"
 
 	"github.com/fsnotify/fsnotify"
@@ -27,6 +28,7 @@ type FileWatcher struct {
 	lastHeadModTime time.Time
 	lastHeadExists bool
 	cancel         context.CancelFunc
+	wg             sync.WaitGroup // Track goroutines for graceful shutdown (bd-jo38)
 }
 
 // NewFileWatcher creates a file watcher for the given JSONL path.
@@ -120,7 +122,9 @@ func (fw *FileWatcher) Start(ctx context.Context, log daemonLogger) {
 		return
 	}
 
+	fw.wg.Add(1)
 	go func() {
+		defer fw.wg.Done()
 		jsonlBase := filepath.Base(fw.jsonlPath)
 
 		for {
@@ -212,7 +216,9 @@ func (fw *FileWatcher) reEstablishWatch(ctx context.Context, log daemonLogger) {
 func (fw *FileWatcher) startPolling(ctx context.Context, log daemonLogger) {
 	log.log("Starting polling mode with %v interval", fw.pollInterval)
 	ticker := time.NewTicker(fw.pollInterval)
+	fw.wg.Add(1)
 	go func() {
+		defer fw.wg.Done()
 		defer ticker.Stop()
 		for {
 			select {
@@ -297,6 +303,8 @@ func (fw *FileWatcher) Close() error {
 	if fw.cancel != nil {
 		fw.cancel()
 	}
+	// Wait for goroutines to finish before cleanup (bd-jo38)
+	fw.wg.Wait()
 	fw.debouncer.Cancel()
 	if fw.watcher != nil {
 		return fw.watcher.Close()

cmd/bd/daemons.go

@@ -248,7 +248,24 @@ Stops the daemon gracefully, then starts a new one.`,
 			os.Exit(1)
 		}
 		// Don't wait for daemon to exit (it will fork and continue in background)
-		go func() { _ = daemonCmd.Wait() }()
+		// Use timeout to prevent goroutine leak if daemon never completes (bd-zqmb)
+		go func() {
+			done := make(chan struct{})
+			go func() {
+				_ = daemonCmd.Wait()
+				close(done)
+			}()
+
+			select {
+			case <-done:
+				// Daemon exited normally (forked successfully)
+			case <-time.After(10 * time.Second):
+				// Timeout - daemon should have forked by now
+				if daemonCmd.Process != nil {
+					_ = daemonCmd.Process.Kill()
+				}
+			}
+		}()
 		if jsonOutput {
 			outputJSON(map[string]interface{}{
 				"workspace": workspace,

cmd/bd/doctor.go

@@ -419,16 +419,8 @@ func checkIDFormat(path string) doctorCheck {
 	}
 	defer func() { _ = db.Close() }() // Intentionally ignore close error
 
-	// Get first issue to check ID format
-	var issueID string
-	err = db.QueryRow("SELECT id FROM issues ORDER BY created_at LIMIT 1").Scan(&issueID)
-	if err == sql.ErrNoRows {
-		return doctorCheck{
-			Name:    "Issue IDs",
-			Status:  statusOK,
-			Message: "No issues yet (will use hash-based IDs)",
-		}
-	}
+	// Get sample of issues to check ID format (up to 10 for pattern analysis)
+	rows, err := db.Query("SELECT id FROM issues ORDER BY created_at LIMIT 10")
 	if err != nil {
 		return doctorCheck{
 			Name:    "Issue IDs",
@@ -436,9 +428,26 @@ func checkIDFormat(path string) doctorCheck {
 			Message: "Unable to query issues",
 		}
 	}
+	defer rows.Close()
 
-	// Detect ID format
-	if isHashID(issueID) {
+	var issueIDs []string
+	for rows.Next() {
+		var id string
+		if err := rows.Scan(&id); err == nil {
+			issueIDs = append(issueIDs, id)
+		}
+	}
+
+	if len(issueIDs) == 0 {
+		return doctorCheck{
+			Name:    "Issue IDs",
+			Status:  statusOK,
+			Message: "No issues yet (will use hash-based IDs)",
+		}
+	}
+
+	// Detect ID format using robust heuristic
+	if detectHashBasedIDs(db, issueIDs) {
 		return doctorCheck{
 			Name:    "Issue IDs",
 			Status:  statusOK,
@@ -522,6 +531,110 @@ func getDatabaseVersionFromPath(dbPath string) string {
 	return "unknown"
 }
 
+// detectHashBasedIDs uses multiple heuristics to determine if the database uses hash-based IDs.
+// This is more robust than checking a single ID's format, since base36 hash IDs can be all-numeric.
+func detectHashBasedIDs(db *sql.DB, sampleIDs []string) bool {
+	// Heuristic 1: Check for child_counters table (added for hash ID support)
+	var tableName string
+	err := db.QueryRow(`
+		SELECT name FROM sqlite_master
+		WHERE type='table' AND name='child_counters'
+	`).Scan(&tableName)
+	if err == nil {
+		// child_counters table exists - this is a strong indicator of hash IDs
+		return true
+	}
+
+	// Heuristic 2: Check if any sample ID clearly contains letters (a-z)
+	// Hash IDs use base36 (0-9, a-z), sequential IDs are purely numeric
+	for _, id := range sampleIDs {
+		if isHashID(id) {
+			return true
+		}
+	}
+
+	// Heuristic 3: Look for patterns that indicate hash IDs
+	if len(sampleIDs) >= 2 {
+		// Extract suffixes (part after prefix-) for analysis
+		var suffixes []string
+		for _, id := range sampleIDs {
+			parts := strings.SplitN(id, "-", 2)
+			if len(parts) == 2 {
+				// Strip hierarchical suffix like .1 or .1.2
+				baseSuffix := strings.Split(parts[1], ".")[0]
+				suffixes = append(suffixes, baseSuffix)
+			}
+		}
+
+		if len(suffixes) >= 2 {
+			// Check for variable lengths (strong indicator of adaptive hash IDs)
+			// BUT: sequential IDs can also have variable length (1, 10, 100)
+			// So we need to check if the length variation is natural (1→2→3 digits)
+			// or random (3→8→4 chars typical of adaptive hash IDs)
+			lengths := make(map[int]int) // length -> count
+			for _, s := range suffixes {
+				lengths[len(s)]++
+			}
+			
+			// If we have 3+ different lengths, likely hash IDs (adaptive length)
+			// Sequential IDs typically have 1-2 lengths (e.g., 1-9, 10-99, 100-999)
+			if len(lengths) >= 3 {
+				return true
+			}
+
+			// Check for leading zeros (rare in sequential IDs, common in hash IDs)
+			// Sequential IDs: bd-1, bd-2, bd-10, bd-100
+			// Hash IDs: bd-0088, bd-02a4, bd-05a1
+			hasLeadingZero := false
+			for _, s := range suffixes {
+				if len(s) > 1 && s[0] == '0' {
+					hasLeadingZero = true
+					break
+				}
+			}
+			if hasLeadingZero {
+				return true
+			}
+
+			// Check for non-sequential ordering
+			// Try to parse as integers - if they're not sequential, likely hash IDs
+			allNumeric := true
+			var nums []int
+			for _, s := range suffixes {
+				var num int
+				if _, err := fmt.Sscanf(s, "%d", &num); err == nil {
+					nums = append(nums, num)
+				} else {
+					allNumeric = false
+					break
+				}
+			}
+
+			if allNumeric && len(nums) >= 2 {
+				// Check if they form a roughly sequential pattern (1,2,3 or 10,11,12)
+				// Hash IDs would be more random (e.g., 88, 13452, 676)
+				isSequentialPattern := true
+				for i := 1; i < len(nums); i++ {
+					diff := nums[i] - nums[i-1]
+					// Allow for some gaps (deleted issues), but should be mostly sequential
+					if diff < 0 || diff > 100 {
+						isSequentialPattern = false
+						break
+					}
+				}
+				// If the numbers are NOT sequential, they're likely hash IDs
+				if !isSequentialPattern {
+					return true
+				}
+			}
+		}
+	}
+
+	// If we can't determine for sure, default to assuming sequential IDs
+	// This is conservative - better to recommend migration than miss sequential IDs
+	return false
+}
+
 // Note: isHashID is defined in migrate_hash_ids.go to avoid duplication
 
 // compareVersions compares two semantic version strings.

cmd/bd/doctor_test.go

@@ -1,7 +1,9 @@
 package main
 
 import (
+	"database/sql"
 	"encoding/json"
+	"fmt"
 	"os"
 	"path/filepath"
 	"strings"
@@ -98,6 +100,250 @@ func TestDoctorJSONOutput(t *testing.T) {
 
 // Note: isHashID is tested in migrate_hash_ids_test.go
 
+func TestDetectHashBasedIDs(t *testing.T) {
+	tests := []struct {
+		name      string
+		sampleIDs []string
+		hasTable  bool
+		expected  bool
+	}{
+		{
+			name:      "hash IDs with letters",
+			sampleIDs: []string{"bd-a3f8e9", "bd-b2c4d6"},
+			hasTable:  false,
+			expected:  true,
+		},
+		{
+			name:      "hash IDs with mixed alphanumeric",
+			sampleIDs: []string{"bd-0134cc5a", "bd-abc123"},
+			hasTable:  false,
+			expected:  true,
+		},
+		{
+			name:      "hash IDs all numeric with variable length",
+			sampleIDs: []string{"bd-0088", "bd-0134cc5a", "bd-02a4"},
+			hasTable:  false,
+			expected:  true, // Variable length indicates hash IDs
+		},
+		{
+			name:      "hash IDs with leading zeros",
+			sampleIDs: []string{"bd-0088", "bd-02a4", "bd-05a1"},
+			hasTable:  false,
+			expected:  true, // Leading zeros indicate hash IDs
+		},
+		{
+			name:      "hash IDs all numeric non-sequential",
+			sampleIDs: []string{"bd-0088", "bd-2312", "bd-0458"},
+			hasTable:  false,
+			expected:  true, // Non-sequential pattern
+		},
+		{
+			name:      "sequential IDs",
+			sampleIDs: []string{"bd-1", "bd-2", "bd-3", "bd-4"},
+			hasTable:  false,
+			expected:  false, // Sequential pattern
+		},
+		{
+			name:      "sequential IDs with gaps",
+			sampleIDs: []string{"bd-1", "bd-5", "bd-10", "bd-15"},
+			hasTable:  false,
+			expected:  false, // Still sequential pattern (small gaps allowed)
+		},
+		{
+			name:      "database with child_counters table",
+			sampleIDs: []string{"bd-1", "bd-2"},
+			hasTable:  true,
+			expected:  true, // child_counters table indicates hash IDs
+		},
+		{
+			name:      "hash IDs with hierarchical children",
+			sampleIDs: []string{"bd-a3f8e9.1", "bd-a3f8e9.2", "bd-b2c4d6"},
+			hasTable:  false,
+			expected:  true, // Base IDs have letters
+		},
+		{
+			name:      "edge case: single ID with letters",
+			sampleIDs: []string{"bd-abc"},
+			hasTable:  false,
+			expected:  true,
+		},
+		{
+			name:      "edge case: single sequential ID",
+			sampleIDs: []string{"bd-1"},
+			hasTable:  false,
+			expected:  false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			// Create temporary database
+			tmpDir := t.TempDir()
+			dbPath := filepath.Join(tmpDir, "test.db")
+
+			// Open database and create schema
+			db, err := sql.Open("sqlite3", dbPath)
+			if err != nil {
+				t.Fatalf("Failed to open database: %v", err)
+			}
+			defer db.Close()
+
+			// Create issues table
+			_, err = db.Exec(`
+				CREATE TABLE IF NOT EXISTS issues (
+					id TEXT PRIMARY KEY,
+					title TEXT,
+					created_at TIMESTAMP
+				)
+			`)
+			if err != nil {
+				t.Fatalf("Failed to create issues table: %v", err)
+			}
+
+			// Create child_counters table if test requires it
+			if tt.hasTable {
+				_, err = db.Exec(`
+					CREATE TABLE IF NOT EXISTS child_counters (
+						parent_id TEXT PRIMARY KEY,
+						last_child INTEGER NOT NULL DEFAULT 0
+					)
+				`)
+				if err != nil {
+					t.Fatalf("Failed to create child_counters table: %v", err)
+				}
+			}
+
+			// Insert sample issues
+			for _, id := range tt.sampleIDs {
+				_, err = db.Exec("INSERT INTO issues (id, title, created_at) VALUES (?, ?, datetime('now'))",
+					id, "Test issue")
+				if err != nil {
+					t.Fatalf("Failed to insert issue %s: %v", id, err)
+				}
+			}
+
+			// Test detection
+			result := detectHashBasedIDs(db, tt.sampleIDs)
+			if result != tt.expected {
+				t.Errorf("detectHashBasedIDs() = %v, want %v", result, tt.expected)
+			}
+		})
+	}
+}
+
+func TestCheckIDFormat(t *testing.T) {
+	tests := []struct {
+		name           string
+		issueIDs       []string
+		createTable    bool // create child_counters table
+		expectedStatus string
+	}{
+		{
+			name:           "hash IDs with letters",
+			issueIDs:       []string{"bd-a3f8e9", "bd-b2c4d6", "bd-xyz123"},
+			createTable:    false,
+			expectedStatus: statusOK,
+		},
+		{
+			name:           "hash IDs all numeric with leading zeros",
+			issueIDs:       []string{"bd-0088", "bd-02a4", "bd-05a1", "bd-0458"},
+			createTable:    false,
+			expectedStatus: statusOK,
+		},
+		{
+			name:           "hash IDs with child_counters table",
+			issueIDs:       []string{"bd-123", "bd-456"},
+			createTable:    true,
+			expectedStatus: statusOK,
+		},
+		{
+			name:           "sequential IDs",
+			issueIDs:       []string{"bd-1", "bd-2", "bd-3", "bd-4"},
+			createTable:    false,
+			expectedStatus: statusWarning,
+		},
+		{
+			name:           "mixed: mostly hash IDs",
+			issueIDs:       []string{"bd-0088", "bd-0134cc5a", "bd-02a4"},
+			createTable:    false,
+			expectedStatus: statusOK, // Variable length = hash IDs
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			// Create temporary workspace
+			tmpDir := t.TempDir()
+			beadsDir := filepath.Join(tmpDir, ".beads")
+			if err := os.Mkdir(beadsDir, 0750); err != nil {
+				t.Fatal(err)
+			}
+
+			// Create database
+			dbPath := filepath.Join(beadsDir, "beads.db")
+			db, err := sql.Open("sqlite3", dbPath)
+			if err != nil {
+				t.Fatalf("Failed to open database: %v", err)
+			}
+			defer db.Close()
+
+			// Create schema
+			_, err = db.Exec(`
+				CREATE TABLE IF NOT EXISTS issues (
+					id TEXT PRIMARY KEY,
+					title TEXT NOT NULL,
+					created_at TIMESTAMP DEFAULT CURRENT_TIMESTAMP
+				)
+			`)
+			if err != nil {
+				t.Fatalf("Failed to create issues table: %v", err)
+			}
+
+			if tt.createTable {
+				_, err = db.Exec(`
+					CREATE TABLE IF NOT EXISTS child_counters (
+						parent_id TEXT PRIMARY KEY,
+						last_child INTEGER NOT NULL DEFAULT 0
+					)
+				`)
+				if err != nil {
+					t.Fatalf("Failed to create child_counters table: %v", err)
+				}
+			}
+
+			// Insert test issues
+			for i, id := range tt.issueIDs {
+				_, err = db.Exec(
+					"INSERT INTO issues (id, title, created_at) VALUES (?, ?, datetime('now', ?||' seconds'))",
+					id, "Test issue "+id, fmt.Sprintf("+%d", i))
+				if err != nil {
+					t.Fatalf("Failed to insert issue %s: %v", id, err)
+				}
+			}
+			db.Close()
+
+			// Run check
+			check := checkIDFormat(tmpDir)
+
+			if check.Status != tt.expectedStatus {
+				t.Errorf("Expected status %s, got %s (message: %s)", tt.expectedStatus, check.Status, check.Message)
+			}
+
+			if tt.expectedStatus == statusOK && check.Status == statusOK {
+				if !strings.Contains(check.Message, "hash-based") {
+					t.Errorf("Expected hash-based message, got: %s", check.Message)
+				}
+			}
+
+			if tt.expectedStatus == statusWarning && check.Status == statusWarning {
+				if check.Fix == "" {
+					t.Error("Expected fix message for sequential IDs")
+				}
+			}
+		})
+	}
+}
+
 func TestCheckInstallation(t *testing.T) {
 	// Test with missing .beads directory
 	tmpDir := t.TempDir()

cmd/bd/migrate_hash_ids_test.go

@@ -251,13 +251,33 @@ func TestIsHashID(t *testing.T) {
 		id       string
 		expected bool
 	}{
+		// Sequential IDs (numeric only, short)
 		{"bd-1", false},
 		{"bd-123", false},
+		{"bd-9999", false},
+		
+		// Hash IDs with letters
 		{"bd-a3f8e9a2", true},
 		{"bd-abc123", true},
 		{"bd-123abc", true},
 		{"bd-a3f8e9a2.1", true},
 		{"bd-a3f8e9a2.1.2", true},
+		
+		// Hash IDs that are numeric but 5+ characters (likely hash)
+		{"bd-12345", true},
+		{"bd-0088", false}, // 4 chars, all numeric - ambiguous, defaults to false
+		{"bd-00880", true},  // 5+ chars, likely hash
+		
+		// Base36 hash IDs with letters
+		{"bd-5n3", true},
+		{"bd-65w", true},
+		{"bd-jmx", true},
+		{"bd-4rt", true},
+		
+		// Edge cases
+		{"bd-", false},     // Empty suffix
+		{"invalid", false}, // No dash
+		{"bd-0", false},    // Single digit
 	}
 
 	for _, tt := range tests {

cmd/bd/show.go

@@ -34,7 +34,12 @@ var showCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving ID %s: %v\n", id, err)
 					os.Exit(1)
 				}
-				resolvedIDs = append(resolvedIDs, string(resp.Data))
+				var resolvedID string
+				if err := json.Unmarshal(resp.Data, &resolvedID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					os.Exit(1)
+				}
+				resolvedIDs = append(resolvedIDs, resolvedID)
 			}
 		} else {
 			// In direct mode, resolve via storage
@@ -392,7 +397,12 @@ var updateCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving ID %s: %v\n", id, err)
 					os.Exit(1)
 				}
-				resolvedIDs = append(resolvedIDs, string(resp.Data))
+				var resolvedID string
+				if err := json.Unmarshal(resp.Data, &resolvedID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					os.Exit(1)
+				}
+				resolvedIDs = append(resolvedIDs, resolvedID)
 			}
 		} else {
 			var err error
@@ -711,7 +721,12 @@ var closeCmd = &cobra.Command{
 					fmt.Fprintf(os.Stderr, "Error resolving ID %s: %v\n", id, err)
 					os.Exit(1)
 				}
-				resolvedIDs = append(resolvedIDs, string(resp.Data))
+				var resolvedID string
+				if err := json.Unmarshal(resp.Data, &resolvedID); err != nil {
+					fmt.Fprintf(os.Stderr, "Error unmarshaling resolved ID: %v\n", err)
+					os.Exit(1)
+				}
+				resolvedIDs = append(resolvedIDs, resolvedID)
 			}
 		} else {
 			var err error

go.mod

@@ -5,14 +5,15 @@ go 1.24.0
 toolchain go1.24.2
 
 require (
-	github.com/anthropics/anthropic-sdk-go v1.17.0
+	github.com/anthropics/anthropic-sdk-go v1.18.0
 	github.com/fatih/color v1.18.0
 	github.com/fsnotify/fsnotify v1.9.0
 	github.com/google/go-cmp v0.7.0
 	github.com/ncruces/go-sqlite3 v0.30.1
 	github.com/spf13/cobra v1.10.1
 	github.com/spf13/viper v1.21.0
-	golang.org/x/mod v0.29.0
+	github.com/tetratelabs/wazero v1.10.0
+	golang.org/x/mod v0.30.0
 	golang.org/x/sys v0.38.0
 	gopkg.in/natefinch/lumberjack.v2 v2.2.1
 	gopkg.in/yaml.v3 v3.0.1
@@ -32,12 +33,11 @@ require (
 	github.com/spf13/cast v1.10.0 // indirect
 	github.com/spf13/pflag v1.0.10 // indirect
 	github.com/subosito/gotenv v1.6.0 // indirect
-	github.com/tetratelabs/wazero v1.10.0 // indirect
 	github.com/tidwall/gjson v1.18.0 // indirect
 	github.com/tidwall/match v1.1.1 // indirect
 	github.com/tidwall/pretty v1.2.1 // indirect
 	github.com/tidwall/sjson v1.2.5 // indirect
 	go.yaml.in/yaml/v3 v3.0.4 // indirect
 	golang.org/x/text v0.30.0 // indirect
-	golang.org/x/tools v0.37.0 // indirect
+	golang.org/x/tools v0.38.0 // indirect
 )

go.sum

@@ -1,5 +1,5 @@
-github.com/anthropics/anthropic-sdk-go v1.17.0 h1:BwK8ApcmaAUkvZTiQE0yi3R9XneEFskDIjLTmOAFZxQ=
-github.com/anthropics/anthropic-sdk-go v1.17.0/go.mod h1:WTz31rIUHUHqai2UslPpw5CwXrQP3geYBioRV4WOLvE=
+github.com/anthropics/anthropic-sdk-go v1.18.0 h1:jfxRA7AqZoCm83nHO/OVQp8xuwjUKtBziEdMbfmofHU=
+github.com/anthropics/anthropic-sdk-go v1.18.0/go.mod h1:WTz31rIUHUHqai2UslPpw5CwXrQP3geYBioRV4WOLvE=
 github.com/cpuguy83/go-md2man/v2 v2.0.6/go.mod h1:oOW0eioCTA6cOiMLiUPZOpcVxMig6NIQQ7OS05n1F4g=
 github.com/davecgh/go-spew v1.1.1 h1:vj9j/u1bqnvCEfJOwUhtlOARqs3+rkHYY13jYWTU97c=
 github.com/davecgh/go-spew v1.1.1/go.mod h1:J7Y8YcW2NihsgmVo/mv3lAwl/skON4iLHjSsI+c5H38=
@@ -68,16 +68,16 @@ github.com/tidwall/sjson v1.2.5 h1:kLy8mja+1c9jlljvWTlSazM7cKDRfJuR/bOJhcY5NcY=
 github.com/tidwall/sjson v1.2.5/go.mod h1:Fvgq9kS/6ociJEDnK0Fk1cpYF4FIW6ZF7LAe+6jwd28=
 go.yaml.in/yaml/v3 v3.0.4 h1:tfq32ie2Jv2UxXFdLJdh3jXuOzWiL1fo0bu/FbuKpbc=
 go.yaml.in/yaml/v3 v3.0.4/go.mod h1:DhzuOOF2ATzADvBadXxruRBLzYTpT36CKvDb3+aBEFg=
-golang.org/x/mod v0.29.0 h1:HV8lRxZC4l2cr3Zq1LvtOsi/ThTgWnUk/y64QSs8GwA=
-golang.org/x/mod v0.29.0/go.mod h1:NyhrlYXJ2H4eJiRy/WDBO6HMqZQ6q9nk4JzS3NuCK+w=
+golang.org/x/mod v0.30.0 h1:fDEXFVZ/fmCKProc/yAXXUijritrDzahmwwefnjoPFk=
+golang.org/x/mod v0.30.0/go.mod h1:lAsf5O2EvJeSFMiBxXDki7sCgAxEUcZHXoXMKT4GJKc=
 golang.org/x/sys v0.0.0-20220811171246-fbc7d0a398ab/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.6.0/go.mod h1:oPkhp1MJrh7nUepCBck5+mAzfO9JrbApNNgaTdGDITg=
 golang.org/x/sys v0.38.0 h1:3yZWxaJjBmCWXqhN1qh02AkOnCQ1poK6oF+a7xWL6Gc=
 golang.org/x/sys v0.38.0/go.mod h1:OgkHotnGiDImocRcuBABYBEXf8A9a87e/uXjp9XT3ks=
 golang.org/x/text v0.30.0 h1:yznKA/E9zq54KzlzBEAWn1NXSQ8DIp/NYMy88xJjl4k=
 golang.org/x/text v0.30.0/go.mod h1:yDdHFIX9t+tORqspjENWgzaCVXgk0yYnYuSZ8UzzBVM=
-golang.org/x/tools v0.37.0 h1:DVSRzp7FwePZW356yEAChSdNcQo6Nsp+fex1SUW09lE=
-golang.org/x/tools v0.37.0/go.mod h1:MBN5QPQtLMHVdvsbtarmTNukZDdgwdwlO5qGacAzF0w=
+golang.org/x/tools v0.38.0 h1:Hx2Xv8hISq8Lm16jvBZ2VQf+RLmbd7wVUsALibYI/IQ=
+golang.org/x/tools v0.38.0/go.mod h1:yEsQ/d/YK8cjh0L6rZlY8tgtlKiBNTL14pGDJPJpYQs=
 gopkg.in/check.v1 v0.0.0-20161208181325-20d25e280405/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15 h1:YR8cESwS4TdDjEe65xsg0ogRM/Nc3DYOhEAlW+xobZo=
 gopkg.in/check.v1 v1.0.0-20190902080502-41f04d3bba15/go.mod h1:Co6ibVJAznAaIkqp8huTwlJQCZ016jof/cbN4VW5Yz0=

integrations/beads-mcp/pyproject.toml

@@ -6,7 +6,7 @@ readme = "README.md"
 requires-python = ">=3.10"
 license = {text = "MIT"}
 dependencies = [
-    "fastmcp==2.13.0.2",
+    "fastmcp==2.13.1",
     "pydantic==2.12.4",
     "pydantic-settings==2.12.0",
 ]

internal/rpc/server_lifecycle_conn.go

@@ -210,7 +210,10 @@ func (s *Server) handleConnection(conn net.Conn) {
 				Success: false,
 				Error:   fmt.Sprintf("invalid request: %v", err),
 			}
-			s.writeResponse(writer, resp)
+			if err := s.writeResponse(writer, resp); err != nil {
+				// Connection broken, stop handling this connection
+				return
+			}
 			continue
 		}
 
@@ -220,15 +223,32 @@ func (s *Server) handleConnection(conn net.Conn) {
 		}
 
 		resp := s.handleRequest(&req)
-		s.writeResponse(writer, resp)
+		if err := s.writeResponse(writer, resp); err != nil {
+			// Connection broken, stop handling this connection
+			return
+		}
 	}
 }
 
-func (s *Server) writeResponse(writer *bufio.Writer, resp Response) {
-	data, _ := json.Marshal(resp)
-	_, _ = writer.Write(data)
-	_ = writer.WriteByte('\n')
-	_ = writer.Flush()
+func (s *Server) writeResponse(writer *bufio.Writer, resp Response) error {
+	data, err := json.Marshal(resp)
+	if err != nil {
+		return fmt.Errorf("failed to marshal response: %w", err)
+	}
+
+	if _, err := writer.Write(data); err != nil {
+		return fmt.Errorf("failed to write response: %w", err)
+	}
+
+	if err := writer.WriteByte('\n'); err != nil {
+		return fmt.Errorf("failed to write newline: %w", err)
+	}
+
+	if err := writer.Flush(); err != nil {
+		return fmt.Errorf("failed to flush response: %w", err)
+	}
+
+	return nil
 }
 
 func (s *Server) handleShutdown(_ *Request) Response {

internal/storage/sqlite/sqlite.go

@@ -8,6 +8,7 @@ import (
 	"fmt"
 	"os"
 	"path/filepath"
+	"runtime"
 	"strings"
 	"sync/atomic"
 	"time"
@@ -113,6 +114,15 @@ func New(path string) (*SQLiteStorage, error) {
 	if isInMemory {
 		db.SetMaxOpenConns(1)
 		db.SetMaxIdleConns(1)
+	} else {
+		// For file-based databases in daemon mode, limit connection pool to prevent
+		// connection exhaustion under concurrent load. SQLite WAL mode supports
+		// 1 writer + unlimited readers, but we limit to prevent goroutine pile-up
+		// on write lock contention (bd-qhws).
+		maxConns := runtime.NumCPU() + 1 // 1 writer + N readers
+		db.SetMaxOpenConns(maxConns)
+		db.SetMaxIdleConns(2)
+		db.SetConnMaxLifetime(0) // SQLite doesn't need connection recycling
 	}
 
 	// For file-based databases, enable WAL mode once after opening the connection.
@@ -1134,11 +1144,11 @@ func (s *SQLiteStorage) findAllDependentsRecursive(ctx context.Context, tx *sql.
 		if err != nil {
 			return nil, err
 		}
+		defer rows.Close()
 
 		for rows.Next() {
 			var depID string
 			if err := rows.Scan(&depID); err != nil {
-				_ = rows.Close()
 				return nil, err
 			}
 			if !result[depID] {
@@ -1147,10 +1157,8 @@ func (s *SQLiteStorage) findAllDependentsRecursive(ctx context.Context, tx *sql.
 			}
 		}
 		if err := rows.Err(); err != nil {
-			_ = rows.Close()
 			return nil, err
 		}
-		_ = rows.Close()
 	}
 
 	return result, nil

internal/utils/id_parser.go

@@ -37,6 +37,14 @@ func ParseIssueID(input string, prefix string) string {
 // - No issue found matching the ID
 // - Multiple issues match (ambiguous prefix)
 func ResolvePartialID(ctx context.Context, store storage.Storage, input string) (string, error) {
+	// Fast path: if the user typed an exact ID that exists, return it as-is.
+	// This preserves behavior where issue IDs may not match the configured
+	// issue_prefix (e.g. cross-repo IDs like "ao-izl"), while still allowing
+	// prefix-based and hash-based resolution for other inputs.
+	if issue, err := store.GetIssue(ctx, input); err == nil && issue != nil {
+		return input, nil
+	}
+	
 	// Get the configured prefix
 	prefix, err := store.GetConfig(ctx, "issue_prefix")
 	if err != nil || prefix == "" {
@@ -63,7 +71,7 @@ func ResolvePartialID(ctx context.Context, store storage.Storage, input string)
 		normalizedID = prefixWithHyphen + input
 	}
 	
-	// First try exact match
+	// First try exact match on normalized ID
 	issue, err := store.GetIssue(ctx, normalizedID)
 	if err == nil && issue != nil {
 		return normalizedID, nil