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/daemons.go

@@ -36,7 +36,7 @@ var daemonsListCmd = &cobra.Command{
 uptime, last activity, and exclusive lock status.`,
 	Run: func(cmd *cobra.Command, args []string) {
 		searchRoots, _ := cmd.Flags().GetStringSlice("search")
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 
 		// Discover daemons
 		daemons, err := daemon.DiscoverDaemons(searchRoots)
@@ -139,7 +139,7 @@ Sends shutdown command via RPC, with SIGTERM fallback if RPC fails.`,
 	Args: cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
 		target := args[0]
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 
 		// Discover all daemons
 		daemons, err := daemon.DiscoverDaemons(nil)
@@ -209,7 +209,7 @@ Supports tail mode (last N lines) and follow mode (like tail -f).`,
 	Args: cobra.ExactArgs(1),
 	Run: func(cmd *cobra.Command, args []string) {
 		target := args[0]
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 		follow, _ := cmd.Flags().GetBool("follow")
 		lines, _ := cmd.Flags().GetInt("lines")
 
@@ -348,7 +348,7 @@ var daemonsKillallCmd = &cobra.Command{
 Uses escalating shutdown strategy: RPC (2s) → SIGTERM (3s) → SIGKILL (1s).`,
 	Run: func(cmd *cobra.Command, args []string) {
 		searchRoots, _ := cmd.Flags().GetStringSlice("search")
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 		force, _ := cmd.Flags().GetBool("force")
 
 		// Discover all daemons
@@ -411,7 +411,7 @@ var daemonsHealthCmd = &cobra.Command{
 stale sockets, version mismatches, and unresponsive daemons.`,
 	Run: func(cmd *cobra.Command, args []string) {
 		searchRoots, _ := cmd.Flags().GetStringSlice("search")
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 
 		// Discover daemons
 		daemons, err := daemon.DiscoverDaemons(searchRoots)