Fix config system: rename config.json → metadata.json, fix config.yaml loading

- Renamed config.json to metadata.json to clarify purpose (database metadata)
- Fixed config.yaml/config.json conflict by making Viper explicitly load only config.yaml
- Added automatic migration from config.json to metadata.json on first read
- Fixed jsonOutput variable shadowing across 22 command files
- Updated bd init to create both metadata.json and config.yaml template
- Fixed 5 failing JSON output tests
- All tests passing

Resolves config file confusion and makes config.yaml work correctly.
Closes #178 (global flags), addresses config issues from #193

Amp-Thread-ID: https://ampcode.com/threads/T-e6ac8192-e18f-4ed7-83bc-4a5986718bb7
Co-authored-by: Amp <amp@ampcode.com>

cmd/bd/main.go

@@ -78,6 +78,23 @@ var (
 	noDb         bool // Use --no-db mode: load from JSONL, write back after each command
 )
 
+func init() {
+	// Initialize viper configuration
+	if err := config.Initialize(); err != nil {
+		fmt.Fprintf(os.Stderr, "Warning: failed to initialize config: %v\n", err)
+	}
+
+	// Register persistent flags
+	rootCmd.PersistentFlags().StringVar(&dbPath, "db", "", "Database path (default: auto-discover .beads/*.db)")
+	rootCmd.PersistentFlags().StringVar(&actor, "actor", "", "Actor name for audit trail (default: $BD_ACTOR or $USER)")
+	rootCmd.PersistentFlags().BoolVar(&jsonOutput, "json", false, "Output in JSON format")
+	rootCmd.PersistentFlags().BoolVar(&noDaemon, "no-daemon", false, "Force direct storage mode, bypass daemon if running")
+	rootCmd.PersistentFlags().BoolVar(&noAutoFlush, "no-auto-flush", false, "Disable automatic JSONL sync after CRUD operations")
+	rootCmd.PersistentFlags().BoolVar(&noAutoImport, "no-auto-import", false, "Disable automatic JSONL import when newer than DB")
+	rootCmd.PersistentFlags().BoolVar(&sandboxMode, "sandbox", false, "Sandbox mode: disables daemon and auto-sync")
+	rootCmd.PersistentFlags().BoolVar(&noDb, "no-db", false, "Use no-db mode: load from JSONL, no SQLite")
+}
+
 var rootCmd = &cobra.Command{
 	Use:   "bd",
 	Short: "bd - Dependency-aware issue tracker",