commands

var VarAddCmd = &cobra.Command{
	Use:   "add <repo-url> [branch] [spec-path]",
	Short: "Add a dependency",
	Long:  `Add an external specification dependency to your project. The dependency will be tracked in specledger.yaml and cached locally for offline use.`,
	Example: `  sl deps add git@github.com:org/api-spec
  sl deps add git@github.com:org/api-spec v1.0 github.com/specledger/specledger/api.md
  sl deps add git@github.com:org/api-spec main spec.md --alias api`,
	Args: cobra.MinimumNArgs(1),
	RunE: runAddDependency,
}

var VarBootstrapCmd = &cobra.Command{
	Use:   "new",
	Short: "Create a new SpecLedger project",
	Long: `Create a new SpecLedger project with all necessary infrastructure:

Interactive mode:
  sl new

Non-interactive mode (for CI/CD):
  sl new --ci --project-name <name> --short-code <code> --project-dir <path>

The bootstrap creates:
- .claude/ directory with skills and commands
- .beads/ directory for issue tracking
- github.com/specledger/specledger/ directory for specifications
- github.com/specledger/specledger/specledger.yaml file for project metadata`,

	RunE: func(cmd *cobra.Command, args []string) error {

		cfg, err := config.Load()
		if err != nil {
			return fmt.Errorf("failed to load config: %w", err)
		}

		l := logger.New(logger.Debug)

		modeDetector := tui.NewModeDetector()
		if modeDetector.IsNonInteractive() || ciFlag {
			return runBootstrapNonInteractive(cmd, l, cfg)
		}

		return runBootstrapInteractive(l, cfg)
	},
}

var VarCheckCmd = &cobra.Command{
	Use:   "check",
	Short: "Check for conflicts in the dependency graph",
	RunE:  runCheckConflicts,
}

var VarCleanCmd = &cobra.Command{
	Use:   "clean",
	Short: "Remove vendored dependencies",
	RunE:  runVendorClean,
}

var VarConflictCmd = &cobra.Command{
	Use:   "conflict",
	Short: "Check for dependency conflicts",
	Long:  `Check the dependency graph for potential conflicts and circular dependencies.`,
}

var VarDepsCmd = &cobra.Command{
	Use:   "deps",
	Short: "Manage specification dependencies",
	Long: `Manage external specification dependencies for your project.

Dependencies are stored in github.com/specledger/specledger/specledger.yaml and cached locally for offline use.

Examples:
  sl deps list                           # List all dependencies
  sl deps add git@github.com:org/spec    # Add a dependency
  sl deps remove git@github.com:org/spec # Remove a dependency`,
}

var VarDepsListCmd = &cobra.Command{
	Use:     "list",
	Short:   "List all dependencies",
	Long:    `List all declared dependencies from specledger.yaml, showing their repository, version, and resolved status.`,
	Example: `  sl deps list`,
	RunE:    runListDependencies,
}

var VarDepsUpdateCmd = &cobra.Command{
	Use:   "update [repo-url]",
	Short: "Update dependencies to latest versions",
	Long:  `Update dependencies to their latest versions. If no URL is given, updates all dependencies.`,
	Example: `  sl deps update                    # Update all
  sl deps update git@github.com:org/spec # Update one`,
	RunE: runUpdateDependencies,
}

var VarDetectCmd = &cobra.Command{
	Use:   "detect",
	Short: "Detect potential conflicts",
	RunE:  runDetectConflicts,
}

var VarDoctorCmd = &cobra.Command{
	Use:   "doctor",
	Short: "Check installation status of required and optional tools",
	Long: `Check the installation status of all tools required by SpecLedger.

This command verifies that:
- Core tools (mise, bd, perles) are installed and accessible
- Framework tools (specify, openspec) are installed (optional)

Use --json flag for machine-readable output suitable for CI/CD pipelines.`,
	Example: `  sl doctor           # Human-readable output
  sl doctor --json    # JSON output for CI/CD`,
	RunE:          runDoctor,
	SilenceUsage:  true,
	SilenceErrors: true,
}

var VarExportCmd = &cobra.Command{
	Use:   "export --format <format> --output <file>",
	Short: "Export graph to file (coming soon)",
	Long: `Export the dependency graph to a file for visualization.

Supported formats will include: JSON, SVG, DOT (Graphviz)`,
	Example: "  sl graph export --format svg --output deps.svg",
	RunE:    runExportGraph,
}

var VarGraphCmd = &cobra.Command{
	Use:   "graph",
	Short: "Display dependency graphs",
	Long: `Visualize dependencies and their relationships.

NOTE: This feature is coming soon. For now, use 'sl deps list' to see dependencies.`,
}

var VarInitCmd = &cobra.Command{
	Use:   "init",
	Short: "Initialize SpecLedger in an existing repository",
	Long: `Initialize SpecLedger in the current repository directory.

This adds SpecLedger to an existing project without creating a new directory.

Usage:
  sl init
  sl init --short-code abc
  sl init --playbook specledger

The init creates:
- .claude/ directory with skills
- .beads/ directory for issue tracking
- github.com/specledger/specledger/ directory for specifications
- github.com/specledger/specledger/specledger.yaml file for project metadata`,
	RunE: func(cmd *cobra.Command, args []string) error {
		l := logger.New(logger.Debug)
		return runInit(l)
	},
}

var VarListCmd = &cobra.Command{
	Use:   "list [--spec-path <path>]",
	Short: "List all external references",
	RunE:  runListReferences,
}

var VarPlaybookCmd = &cobra.Command{
	Use:   "playbook",
	Short: "Manage SDD playbooks",
	Long: `Manage embedded SDD playbooks for SpecLedger.

Playbooks contain Claude Code commands, skills, scripts, and templates
for SpecLedger projects.

Examples:
  sl playbook list              List all available playbooks
  sl playbook list --json       List playbooks in JSON format`,
}

var VarPlaybookListCmd = &cobra.Command{
	Use:     "list",
	Short:   "List available SDD playbooks",
	Long:    `List all available embedded SDD playbooks with their names, descriptions, frameworks, and versions.`,
	Example: `  sl playbook list`,
	RunE:    runListPlaybooks,
}

var VarRefsCmd = &cobra.Command{
	Use:   "refs",
	Short: "Validate external specification references",
}

var VarRemoveCmd = &cobra.Command{
	Use:     "remove <repo-url>",
	Short:   "Remove a dependency",
	Long:    `Remove a dependency from specledger.yaml. The local cache will be kept for future use.`,
	Example: `  sl deps remove git@github.com:org/api-spec`,
	Args:    cobra.ExactArgs(1),
	RunE:    runRemoveDependency,
}

var VarResolveCmd = &cobra.Command{
	Use:     "resolve",
	Short:   "Download and cache dependencies",
	Long:    `Download all dependencies from specledger.yaml and cache them locally at ~/.github.com/specledger/specledger/cache/.`,
	Example: `  sl deps resolve`,
	RunE:    runResolveDependencies,
}

var VarShowCmd = &cobra.Command{
	Use:   "show",
	Short: "Show dependency graph (coming soon)",
	Long: `Display the complete dependency graph with all nodes and edges.

This will show how specifications depend on each other.`,
	Example: "  sl graph show",
	RunE:    runShowGraph,
}

var VarTransitiveCmd = &cobra.Command{
	Use:   "transitive",
	Short: "Show transitive dependencies (coming soon)",
	Long: `Show all transitive dependencies up to a specified depth.

This helps understand the full dependency tree.`,
	Example: "  sl graph transitive --depth 3",
	RunE:    runTransitiveDependencies,
}

var VarUpdateCmd = &cobra.Command{
	Use:   "update",
	Short: "Update the SpecLedger CLI to the latest version",
	Long:  `Check for updates and upgrade the SpecLedger CLI to the latest version.`,
	RunE:  runUpdateSelf,
}

var VarValidateCmd = &cobra.Command{
	Use:   "validate [--strict] [--spec-path <path>]",
	Short: "Validate all external references in a specification",
	Long:  `Validate all external references in spec.md files against resolved dependencies.`,
	Args:  cobra.MaximumNArgs(1),
	RunE:  runValidateReferences,
}

var VarVendorAllCmd = &cobra.Command{
	Use:   "vendor --output <path>",
	Short: "Copy all dependencies to vendor directory",
	Long:  `Copy all external dependencies to the local vendor directory for offline use.`,
	Args:  cobra.MaximumNArgs(1),
	RunE:  runVendorAll,
}

var VarVendorCmd = &cobra.Command{
	Use:   "vendor",
	Short: "Vendor dependencies for offline use",
}

var VarVendorUpdateCmd = &cobra.Command{
	Use:   "update [--vendor-path <path>] [--force]",
	Short: "Update vendored dependencies",
	RunE:  runVendorUpdate,
}