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/migrate.go

@@ -100,7 +100,7 @@ This command:
 			return
 		}
 
-		// Check if target database exists and is current (use config.json name)
+		// Check if target database exists and is current (use metadata.json name)
 		targetPath := cfg.DatabasePath(beadsDir)
 		var currentDB *dbInfo
 		var oldDBs []*dbInfo
@@ -444,7 +444,7 @@ This command:
 		if !dryRun {
 			if err := cfg.Save(beadsDir); err != nil {
 				if !jsonOutput {
-					color.Yellow("Warning: failed to update config.json version: %v\n", err)
+					color.Yellow("Warning: failed to update metadata.json version: %v\n", err)
 				}
 				// Don't fail migration if config save fails
 			}
@@ -667,7 +667,7 @@ func handleUpdateRepoID(dryRun bool, autoYes bool) {
 	}
 }
 
-// loadOrCreateConfig loads config.json or creates default if not found
+// loadOrCreateConfig loads metadata.json or creates default if not found
 func loadOrCreateConfig(beadsDir string) (*configfile.Config, error) {
 	cfg, err := configfile.Load(beadsDir)
 	if err != nil {