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>

internal/configfile/configfile.go

@@ -7,7 +7,7 @@ import (
 	"path/filepath"
 )
 
-const ConfigFileName = "config.json"
+const ConfigFileName = "metadata.json"
 
 type Config struct {
 	Database     string `json:"database"`
@@ -32,7 +32,31 @@ func Load(beadsDir string) (*Config, error) {
 	
 	data, err := os.ReadFile(configPath) // #nosec G304 - controlled path from config
 	if os.IsNotExist(err) {
-		return nil, nil
+		// Try legacy config.json location (migration path)
+		legacyPath := filepath.Join(beadsDir, "config.json")
+		data, err = os.ReadFile(legacyPath) // #nosec G304 - controlled path from config
+		if os.IsNotExist(err) {
+			return nil, nil
+		}
+		if err != nil {
+			return nil, fmt.Errorf("reading legacy config: %w", err)
+		}
+		
+		// Migrate: parse legacy config, save as metadata.json, remove old file
+		var cfg Config
+		if err := json.Unmarshal(data, &cfg); err != nil {
+			return nil, fmt.Errorf("parsing legacy config: %w", err)
+		}
+		
+		// Save to new location
+		if err := cfg.Save(beadsDir); err != nil {
+			return nil, fmt.Errorf("migrating config to metadata.json: %w", err)
+		}
+		
+		// Remove legacy file (best effort)
+		_ = os.Remove(legacyPath)
+		
+		return &cfg, nil
 	}
 	if err != nil {
 		return nil, fmt.Errorf("reading config: %w", err)