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/ready.go

@@ -20,7 +20,7 @@ var readyCmd = &cobra.Command{
 		limit, _ := cmd.Flags().GetInt("limit")
 		assignee, _ := cmd.Flags().GetString("assignee")
 		sortPolicy, _ := cmd.Flags().GetString("sort")
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun (respects config.yaml + env vars)
 
 		filter := types.WorkFilter{
 			// Leave Status empty to get both 'open' and 'in_progress' (bd-165)
@@ -153,7 +153,7 @@ var blockedCmd = &cobra.Command{
 	Use:   "blocked",
 	Short: "Show blocked issues",
 	Run: func(cmd *cobra.Command, args []string) {
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun (respects config.yaml + env vars)
 		
 		// If daemon is running but doesn't support this command, use direct storage
 		if daemonClient != nil && store == nil {
@@ -208,7 +208,7 @@ var statsCmd = &cobra.Command{
 	Use:   "stats",
 	Short: "Show statistics",
 	Run: func(cmd *cobra.Command, args []string) {
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun (respects config.yaml + env vars)
 
 		// If daemon is running, use RPC
 		if daemonClient != nil {