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/show_test.go

@@ -125,6 +125,8 @@ func TestShowCommand(t *testing.T) {
 		os.Stdout = w
 
 		// Reset command state
+		jsonOutput = true
+		defer func() { jsonOutput = false }()
 		rootCmd.SetArgs([]string{"show", issue1.ID, "--json"})
 
 		err := rootCmd.Execute()
@@ -171,6 +173,8 @@ func TestShowCommand(t *testing.T) {
 		os.Stdout = w
 
 		// Reset command state
+		jsonOutput = true
+		defer func() { jsonOutput = false }()
 		rootCmd.SetArgs([]string{"show", issue1.ID, issue2.ID, "--json"})
 
 		err := rootCmd.Execute()
@@ -204,6 +208,8 @@ func TestShowCommand(t *testing.T) {
 		os.Stdout = w
 
 		// Reset command state
+		jsonOutput = true
+		defer func() { jsonOutput = false }()
 		rootCmd.SetArgs([]string{"show", issue2.ID, "--json"})
 
 		err := rootCmd.Execute()
@@ -490,6 +496,8 @@ func TestUpdateCommand(t *testing.T) {
 		os.Stdout = w
 
 		// Reset command state
+		jsonOutput = true
+		defer func() { jsonOutput = false }()
 		rootCmd.SetArgs([]string{"update", issue.ID, "--priority", "3", "--json"})
 
 		err := rootCmd.Execute()
@@ -779,6 +787,8 @@ func TestCloseCommand(t *testing.T) {
 		os.Stdout = w
 
 		// Reset command state
+		jsonOutput = true
+		defer func() { jsonOutput = false }()
 		rootCmd.SetArgs([]string{"close", issue.ID, "--reason", "Fixed", "--json"})
 
 		err := rootCmd.Execute()