chore: use cobra flag group for config flags

cmd/internal/flags.go

@@ -42,7 +42,7 @@ func PersistentFlags(parentCmd *cobra.Command, opts *ToolboxOptions) {
 
 // ConfigFileFlags defines flags related to the configuration file.
 // It should be applied to any command that requires configuration loading.
-func ConfigFileFlags(flags *pflag.FlagSet, opts *ToolboxOptions) {
+func ConfigFileFlags(parentCmd *cobra.Command, flags *pflag.FlagSet, opts *ToolboxOptions) {
 	flags.StringVar(&opts.Config, "config", "", "File path specifying the tool configuration. Cannot be used with --configs, or --config-folder.")
 	flags.StringVar(&opts.Config, "tools-file", "", "File path specifying the tool configuration. Cannot be used with --tools-files, or --tools-folder.")
 	_ = flags.MarkDeprecated("tools-file", "please use --config instead") // DEPRECATED
@@ -52,6 +52,7 @@ func ConfigFileFlags(flags *pflag.FlagSet, opts *ToolboxOptions) {
 	flags.StringVar(&opts.ConfigFolder, "config-folder", "", "Directory path containing YAML tool configuration files. All .yaml and .yml files in the directory will be loaded and merged. Cannot be used with --config, or --configs.")
 	flags.StringVar(&opts.ConfigFolder, "tools-folder", "", "Directory path containing YAML tool configuration files. All .yaml and .yml files in the directory will be loaded and merged. Cannot be used with --tools-file, or --tools-files.")
 	_ = flags.MarkDeprecated("tools-folder", "please use --config-folder instead") // DEPRECATED
+	parentCmd.MarkFlagsMutuallyExclusive("config", "configs", "config-folder")
 	// Fetch prebuilt tools sources to customize the help description
 	prebuiltHelp := fmt.Sprintf(
 		"Use a prebuilt tool configuration by source type. Allowed: '%s'. Can be specified multiple times.",

cmd/internal/invoke/command.go

@@ -42,7 +42,7 @@ Example:
 		},
 	}
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd, flags, opts)
 	return cmd
 }
 

cmd/internal/migrate/command.go

@@ -39,7 +39,7 @@ func NewCommand(opts *internal.ToolboxOptions) *cobra.Command {
 		Long:  "Migrate all configuration files provided to the flat format, updating deprecated fields and ensuring compatibility.",
 	}
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd.Command, flags, opts)
 	flags.BoolVar(&cmd.dryRun, "dry-run", false, "Preview the converted format without applying actual changes.")
 	cmd.RunE = func(*cobra.Command, []string) error { return runMigrate(cmd, opts) }
 	return cmd.Command

cmd/internal/skills/command.go

@@ -57,7 +57,7 @@ func NewCommand(opts *internal.ToolboxOptions) *cobra.Command {
 	}
 
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd.Command, flags, opts)
 	flags.StringVar(&cmd.name, "name", "", "Name of the generated skill.")
 	flags.StringVar(&cmd.description, "description", "", "Description of the generated skill")
 	flags.StringVar(&cmd.toolset, "toolset", "", "Name of the toolset to convert into a skill. If not provided, all tools will be included.")

cmd/root.go

@@ -116,7 +116,7 @@ func NewCommand(opts *internal.ToolboxOptions) *cobra.Command {
 	// setup flags that are common across all commands
 	internal.PersistentFlags(cmd, opts)
 	flags := cmd.Flags()
-	internal.ConfigFileFlags(flags, opts)
+	internal.ConfigFileFlags(cmd, flags, opts)
 	internal.ServeFlags(flags, opts)
 	flags.BoolVar(&opts.Cfg.DisableReload, "disable-reload", false, "Disables dynamic reloading of tools file.")
 	flags.BoolVar(&opts.Cfg.IgnoreUnknownTools, "ignore-unknown-tools", false, "Log warnings and skip unknown/unsupported tool types instead of failing to start.")