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/stale.go

@@ -26,7 +26,7 @@ This helps identify:
 		days, _ := cmd.Flags().GetInt("days")
 		status, _ := cmd.Flags().GetString("status")
 		limit, _ := cmd.Flags().GetInt("limit")
-		jsonOutput, _ := cmd.Flags().GetBool("json")
+		// Use global jsonOutput set by PersistentPreRun
 
 		// Validate status if provided
 		if status != "" && status != "open" && status != "in_progress" && status != "blocked" {