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>

internal/configfile/configfile_test.go

@@ -120,7 +120,7 @@ func TestJSONLPath(t *testing.T) {
 func TestConfigPath(t *testing.T) {
 	beadsDir := "/home/user/project/.beads"
 	got := ConfigPath(beadsDir)
-	want := filepath.Join(beadsDir, "config.json")
+	want := filepath.Join(beadsDir, "metadata.json")
 	
 	if got != want {
 		t.Errorf("ConfigPath() = %q, want %q", got, want)