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/doctor.go

@@ -63,8 +63,7 @@ Examples:
   bd doctor /path/to/repo # Check specific repository
   bd doctor --json       # Machine-readable output`,
 	Run: func(cmd *cobra.Command, args []string) {
-		// Get json flag from command
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 
 		// Determine path to check
 		checkPath := "."
@@ -201,7 +200,7 @@ func checkInstallation(path string) doctorCheck {
 func checkDatabaseVersion(path string) doctorCheck {
 	beadsDir := filepath.Join(path, ".beads")
 	
-	// Check config.json first for custom database name
+	// Check metadata.json first for custom database name
 	var dbPath string
 	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
 		dbPath = cfg.DatabasePath(beadsDir)
@@ -275,7 +274,7 @@ func checkDatabaseVersion(path string) doctorCheck {
 func checkIDFormat(path string) doctorCheck {
 	beadsDir := filepath.Join(path, ".beads")
 	
-	// Check config.json first for custom database name
+	// Check metadata.json first for custom database name
 	var dbPath string
 	if cfg, err := configfile.Load(beadsDir); err == nil && cfg != nil && cfg.Database != "" {
 		dbPath = cfg.DatabasePath(beadsDir)