Adjust sync timings for better batching behavior

- Increase flush debounce from 1s to 30s (provides transaction window for batch operations)
- Increase daemon poll from 2s to 5s (reduces commit spam)
- Agents should run 'bd sync' at end of session to force immediate commit
- Prevents creating dozens of commits when making multiple issue changes

cmd/bd/daemon.go

@@ -29,7 +29,7 @@ var daemonCmd = &cobra.Command{
 	Long: `Run a background daemon that automatically syncs issues with git remote.
 
 The daemon will:
-- Poll for changes at configurable intervals (default: 2 seconds)
+- Poll for changes at configurable intervals (default: 5 seconds)
 - Export pending database changes to JSONL
 - Auto-commit changes if --auto-commit flag set
 - Auto-push commits if --auto-push flag set
@@ -172,7 +172,7 @@ Use --health to check daemon health and metrics.`,
 }
 
 func init() {
-	daemonCmd.Flags().Duration("interval", 2*time.Second, "Sync check interval")
+	daemonCmd.Flags().Duration("interval", 5*time.Second, "Sync check interval")
 	daemonCmd.Flags().Bool("auto-commit", false, "Automatically commit changes")
 	daemonCmd.Flags().Bool("auto-push", false, "Automatically push commits")
 	daemonCmd.Flags().Bool("stop", false, "Stop running daemon")

cmd/bd/main.go

@@ -462,12 +462,12 @@ var rootCmd = &cobra.Command{
 
 // getDebounceDuration returns the auto-flush debounce duration
 // Configurable via config file or BEADS_FLUSH_DEBOUNCE env var (e.g., "500ms", "10s")
-// Defaults to 1 second if not set or invalid
+// Defaults to 30 seconds if not set or invalid (provides batching window)
 func getDebounceDuration() time.Duration {
 	duration := config.GetDuration("flush-debounce")
 	if duration == 0 {
 		// If parsing failed, use default
-		return 1 * time.Second
+		return 30 * time.Second
 	}
 	return duration
 }

internal/config/config.go

@@ -80,7 +80,7 @@ func Initialize() error {
 	_ = v.BindEnv("auto-start-daemon", "BEADS_AUTO_START_DAEMON")
 	
 	// Set defaults for additional settings
-	v.SetDefault("flush-debounce", "1s")
+	v.SetDefault("flush-debounce", "30s")
 	v.SetDefault("auto-start-daemon", true)
 
 	// Read config file if it exists (don't error if not found)