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/label.go

@@ -79,7 +79,7 @@ var labelAddCmd = &cobra.Command{
 	Short: "Add a label to one or more issues",
 	Args:  cobra.MinimumNArgs(2),
 	Run: func(cmd *cobra.Command, args []string) {
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 		issueIDs, label := parseLabelArgs(args)
 		
 		// Resolve partial IDs
@@ -125,7 +125,7 @@ var labelRemoveCmd = &cobra.Command{
 	Short: "Remove a label from one or more issues",
 	Args:  cobra.MinimumNArgs(2),
 	Run: func(cmd *cobra.Command, args []string) {
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 		issueIDs, label := parseLabelArgs(args)
 		
 		// Resolve partial IDs
@@ -170,7 +170,7 @@ var labelListCmd = &cobra.Command{
 	Short: "List labels for an issue",
 	Args:  cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 		ctx := context.Background()
 		
 		// Resolve partial ID first
@@ -245,7 +245,7 @@ var labelListAllCmd = &cobra.Command{
 	Use:   "list-all",
 	Short: "List all unique labels in the database",
 	Run: func(cmd *cobra.Command, args []string) {
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 		ctx := context.Background()
 
 		var issues []*types.Issue