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/config/config.go

@@ -17,43 +17,50 @@ var v *viper.Viper
 func Initialize() error {
 	v = viper.New()
 
-	// Set config file name and type
-	v.SetConfigName("config")
+	// Set config type to yaml (we only load config.yaml, not config.json)
 	v.SetConfigType("yaml")
 
-	// Add config search paths (in order of precedence)
-	// 1. Walk up from CWD to find project .beads/ directory
+	// Explicitly locate config.yaml and use SetConfigFile to avoid picking up config.json
+	// Precedence: project .beads/config.yaml > ~/.config/bd/config.yaml > ~/.beads/config.yaml
+	configFileSet := false
+
+	// 1. Walk up from CWD to find project .beads/config.yaml
 	//    This allows commands to work from subdirectories
 	cwd, err := os.Getwd()
-	if err == nil {
+	if err == nil && !configFileSet {
 		// Walk up parent directories to find .beads/config.yaml
 		for dir := cwd; dir != filepath.Dir(dir); dir = filepath.Dir(dir) {
 			beadsDir := filepath.Join(dir, ".beads")
 			configPath := filepath.Join(beadsDir, "config.yaml")
 			if _, err := os.Stat(configPath); err == nil {
-				// Found .beads/config.yaml - add this path
-				v.AddConfigPath(beadsDir)
-				break
-			}
-			// Also check if .beads directory exists (even without config.yaml)
-			if info, err := os.Stat(beadsDir); err == nil && info.IsDir() {
-				v.AddConfigPath(beadsDir)
+				// Found .beads/config.yaml - set it explicitly
+				v.SetConfigFile(configPath)
+				configFileSet = true
 				break
 			}
 		}
-		
-		// Also add CWD/.beads for backward compatibility
-		v.AddConfigPath(filepath.Join(cwd, ".beads"))
 	}
 
-	// 2. User config directory (~/.config/bd/)
-	if configDir, err := os.UserConfigDir(); err == nil {
-		v.AddConfigPath(filepath.Join(configDir, "bd"))
+	// 2. User config directory (~/.config/bd/config.yaml)
+	if !configFileSet {
+		if configDir, err := os.UserConfigDir(); err == nil {
+			configPath := filepath.Join(configDir, "bd", "config.yaml")
+			if _, err := os.Stat(configPath); err == nil {
+				v.SetConfigFile(configPath)
+				configFileSet = true
+			}
+		}
 	}
 
-	// 3. Home directory (~/.beads/)
-	if homeDir, err := os.UserHomeDir(); err == nil {
-		v.AddConfigPath(filepath.Join(homeDir, ".beads"))
+	// 3. Home directory (~/.beads/config.yaml)
+	if !configFileSet {
+		if homeDir, err := os.UserHomeDir(); err == nil {
+			configPath := filepath.Join(homeDir, ".beads", "config.yaml")
+			if _, err := os.Stat(configPath); err == nil {
+				v.SetConfigFile(configPath)
+				configFileSet = true
+			}
+		}
 	}
 
 	// Automatic environment variable binding
@@ -85,13 +92,19 @@ func Initialize() error {
 	v.SetDefault("flush-debounce", "30s")
 	v.SetDefault("auto-start-daemon", true)
 
-	// Read config file if it exists (don't error if not found)
-	if err := v.ReadInConfig(); err != nil {
-		if _, ok := err.(viper.ConfigFileNotFoundError); !ok {
-			// Config file found but another error occurred
+	// Read config file if it was found
+	if configFileSet {
+		if err := v.ReadInConfig(); err != nil {
 			return fmt.Errorf("error reading config file: %w", err)
 		}
-		// Config file not found - this is ok, we'll use defaults
+		if os.Getenv("BD_DEBUG") != "" {
+			fmt.Fprintf(os.Stderr, "Debug: loaded config from %s\n", v.ConfigFileUsed())
+		}
+	} else {
+		// No config.yaml found - use defaults and environment variables
+		if os.Getenv("BD_DEBUG") != "" {
+			fmt.Fprintf(os.Stderr, "Debug: no config.yaml found; using defaults and environment variables\n")
+		}
 	}
 
 	return nil

internal/configfile/configfile.go

@@ -7,7 +7,7 @@ import (
 	"path/filepath"
 )
 
-const ConfigFileName = "config.json"
+const ConfigFileName = "metadata.json"
 
 type Config struct {
 	Database     string `json:"database"`
@@ -32,7 +32,31 @@ func Load(beadsDir string) (*Config, error) {
 	
 	data, err := os.ReadFile(configPath) // #nosec G304 - controlled path from config
 	if os.IsNotExist(err) {
-		return nil, nil
+		// Try legacy config.json location (migration path)
+		legacyPath := filepath.Join(beadsDir, "config.json")
+		data, err = os.ReadFile(legacyPath) // #nosec G304 - controlled path from config
+		if os.IsNotExist(err) {
+			return nil, nil
+		}
+		if err != nil {
+			return nil, fmt.Errorf("reading legacy config: %w", err)
+		}
+		
+		// Migrate: parse legacy config, save as metadata.json, remove old file
+		var cfg Config
+		if err := json.Unmarshal(data, &cfg); err != nil {
+			return nil, fmt.Errorf("parsing legacy config: %w", err)
+		}
+		
+		// Save to new location
+		if err := cfg.Save(beadsDir); err != nil {
+			return nil, fmt.Errorf("migrating config to metadata.json: %w", err)
+		}
+		
+		// Remove legacy file (best effort)
+		_ = os.Remove(legacyPath)
+		
+		return &cfg, nil
 	}
 	if err != nil {
 		return nil, fmt.Errorf("reading config: %w", err)

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)