Fix multiple issues and renumber database

- bd-170: Implement hybrid sorting for ready work (recent 48h first, then oldest)
- bd-87: Use safer null-byte placeholders in ID remapping
- bd-92: Make auto-flush debounce configurable via BEADS_FLUSH_DEBOUNCE
- bd-171: Fix nil pointer dereference in renumber command
- Delete spurious test issues (bd-7, bd-130-134)
- Renumber database from 171 down to 144 issues

cmd/bd/main.go

@@ -43,7 +43,6 @@ var (
 	needsFullExport   = false // Set to true when IDs change (renumber, rename-prefix)
 	flushMutex        sync.Mutex
 	flushTimer        *time.Timer
-	flushDebounce     = 5 * time.Second
 	storeMutex        sync.Mutex // Protects store access from background goroutine
 	storeActive       = false    // Tracks if store is available
 	flushFailureCount = 0        // Consecutive flush failures
@@ -189,6 +188,24 @@ var rootCmd = &cobra.Command{
 	},
 }
 
+// getDebounceDuration returns the auto-flush debounce duration
+// Configurable via BEADS_FLUSH_DEBOUNCE (e.g., "500ms", "10s")
+// Defaults to 5 seconds if not set or invalid
+func getDebounceDuration() time.Duration {
+	envVal := os.Getenv("BEADS_FLUSH_DEBOUNCE")
+	if envVal == "" {
+		return 5 * time.Second
+	}
+	
+	duration, err := time.ParseDuration(envVal)
+	if err != nil {
+		fmt.Fprintf(os.Stderr, "Warning: invalid BEADS_FLUSH_DEBOUNCE value '%s', using default 5s\n", envVal)
+		return 5 * time.Second
+	}
+	
+	return duration
+}
+
 // shouldAutoStartDaemon checks if daemon auto-start is enabled
 func shouldAutoStartDaemon() bool {
 	// Check environment variable (default: true)
@@ -737,7 +754,7 @@ func markDirtyAndScheduleFlush() {
 	}
 
 	// Schedule new flush
-	flushTimer = time.AfterFunc(flushDebounce, func() {
+	flushTimer = time.AfterFunc(getDebounceDuration(), func() {
 		flushToJSONL()
 	})
 }
@@ -761,7 +778,7 @@ func markDirtyAndScheduleFullExport() {
 	}
 
 	// Schedule new flush
-	flushTimer = time.AfterFunc(flushDebounce, func() {
+	flushTimer = time.AfterFunc(getDebounceDuration(), func() {
 		flushToJSONL()
 	})
 }

cmd/bd/main_test.go

@@ -114,9 +114,8 @@ func TestAutoFlushDebounce(t *testing.T) {
 	storeMutex.Unlock()
 
 	// Set short debounce for testing (100ms)
-	originalDebounce := flushDebounce
-	flushDebounce = 100 * time.Millisecond
-	defer func() { flushDebounce = originalDebounce }()
+	os.Setenv("BEADS_FLUSH_DEBOUNCE", "100ms")
+	defer os.Unsetenv("BEADS_FLUSH_DEBOUNCE")
 
 	// Reset auto-flush state
 	autoFlushEnabled = true

cmd/bd/renumber.go

@@ -46,6 +46,22 @@ Risks:
 			os.Exit(1)
 		}
 
+		// Renumber command needs direct access to storage
+		// Ensure we have a direct store connection
+		if store == nil {
+			var err error
+			if dbPath == "" {
+				fmt.Fprintf(os.Stderr, "Error: no database path found\n")
+				os.Exit(1)
+			}
+			store, err = sqlite.New(dbPath)
+			if err != nil {
+				fmt.Fprintf(os.Stderr, "Error: failed to open database: %v\n", err)
+				os.Exit(1)
+			}
+			defer store.Close()
+		}
+
 		ctx := context.Background()
 
 		// Get prefix from config, or derive from first issue if not set