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/migrate_test.go

@@ -127,18 +127,18 @@ func TestFormatDBList(t *testing.T) {
 }
 
 func TestMigrateRespectsConfigJSON(t *testing.T) {
-	// Test that migrate respects custom database name from config.json
+	// Test that migrate respects custom database name from metadata.json
 	tmpDir := t.TempDir()
 	beadsDir := filepath.Join(tmpDir, ".beads")
 	if err := os.MkdirAll(beadsDir, 0750); err != nil {
 		t.Fatalf("Failed to create .beads directory: %v", err)
 	}
 
-	// Create config.json with custom database name
-	configPath := filepath.Join(beadsDir, "config.json")
+	// Create metadata.json with custom database name
+	configPath := filepath.Join(beadsDir, "metadata.json")
 	configData := `{"database": "beady.db", "version": "0.21.1", "jsonl_export": "beady.jsonl"}`
 	if err := os.WriteFile(configPath, []byte(configData), 0600); err != nil {
-		t.Fatalf("Failed to create config.json: %v", err)
+		t.Fatalf("Failed to create metadata.json: %v", err)
 	}
 
 	// Create old database with custom name