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

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)