@swarmify/agents-cli 1.0.0 → 1.1.0

package/dist/index.js

@@ -2,13 +2,62 @@
 import { Command } from 'commander';
 import chalk from 'chalk';
 import ora from 'ora';
-import { checkbox, select } from '@inquirer/prompts';
-import { AGENTS, ALL_AGENT_IDS, MCP_CAPABLE_AGENTS, getAllCliStates, isCliInstalled, isMcpRegistered, registerMcp, unregisterMcp, } from './lib/agents.js';
+import { checkbox, confirm, select } from '@inquirer/prompts';
+import { AGENTS, ALL_AGENT_IDS, MCP_CAPABLE_AGENTS, SKILLS_CAPABLE_AGENTS, HOOKS_CAPABLE_AGENTS, getAllCliStates, isCliInstalled, isMcpRegistered, registerMcp, unregisterMcp, listInstalledMcpsWithScope, promoteMcpToUser, } from './lib/agents.js';
 import { readManifest, writeManifest, createDefaultManifest, MANIFEST_FILENAME, } from './lib/manifest.js';
-import { readState, writeState, ensureAgentsDir, getRepoLocalPath, } from './lib/state.js';
-import { cloneRepo } from './lib/git.js';
-import { discoverSkills, resolveSkillSource, installSkill, uninstallSkill, listInstalledSkills, } from './lib/skills.js';
+import { readState, ensureAgentsDir, getRepoLocalPath, getScope, setScope, removeScope, getScopesByPriority, getScopePriority, } from './lib/state.js';
+import { SCOPE_PRIORITIES, DEFAULT_SYSTEM_REPO } from './lib/types.js';
+import { cloneRepo, parseSource } from './lib/git.js';
+import { discoverCommands, resolveCommandSource, installCommand, uninstallCommand, listInstalledCommandsWithScope, promoteCommandToUser, } from './lib/commands.js';
+import { discoverHooksFromRepo, installHooks, listInstalledHooksWithScope, promoteHookToUser, removeHook, } from './lib/hooks.js';
+import { discoverSkillsFromRepo, installSkill, uninstallSkill, listInstalledSkillsWithScope, promoteSkillToUser, getSkillInfo, getSkillRules, } from './lib/skills.js';
+import { DEFAULT_REGISTRIES } from './lib/types.js';
+import { search as searchRegistries, getRegistries, setRegistry, removeRegistry, resolvePackage, } from './lib/registry.js';
 const program = new Command();
+/**
+ * Ensure at least one scope is configured.
+ * If not, automatically initialize the system scope from DEFAULT_SYSTEM_REPO.
+ * Returns the highest priority scope's source.
+ */
+async function ensureSource(scopeName) {
+    const meta = readState();
+    // If specific scope requested, check if it exists
+    if (scopeName) {
+        const scope = meta.scopes[scopeName];
+        if (scope?.source) {
+            return scope.source;
+        }
+        throw new Error(`Scope '${scopeName}' not configured. Run: agents repo add <source> --scope ${scopeName}`);
+    }
+    // Check if any scope is configured
+    const scopes = getScopesByPriority();
+    if (scopes.length > 0) {
+        // Return highest priority scope's source
+        return scopes[scopes.length - 1].config.source;
+    }
+    // No scopes configured - initialize system scope
+    console.log(chalk.gray(`No repo configured. Initializing system scope from ${DEFAULT_SYSTEM_REPO}...`));
+    const parsed = parseSource(DEFAULT_SYSTEM_REPO);
+    const { commit } = await cloneRepo(DEFAULT_SYSTEM_REPO);
+    setScope('system', {
+        source: DEFAULT_SYSTEM_REPO,
+        branch: parsed.ref || 'main',
+        commit,
+        lastSync: new Date().toISOString(),
+        priority: SCOPE_PRIORITIES.system,
+        readonly: true,
+    });
+    return DEFAULT_SYSTEM_REPO;
+}
+/**
+ * Get repo local path for a scope.
+ */
+function getScopeLocalPath(scopeName) {
+    const scope = getScope(scopeName);
+    if (!scope)
+        return null;
+    return getRepoLocalPath(scope.source);
+}
 program
     .name('agents')
     .description('Dotfiles manager for AI coding agents')
@@ -18,10 +67,11 @@ program
 // =============================================================================
 program
     .command('status')
-    .description('Show sync status, CLI versions, installed skills and MCP servers')
+    .description('Show sync status, CLI versions, installed commands and MCP servers')
     .action(() => {
     const state = readState();
     const cliStates = getAllCliStates();
+    const cwd = process.cwd();
     console.log(chalk.bold('\nAgent CLIs\n'));
     for (const agentId of ALL_AGENT_IDS) {
         const agent = AGENTS[agentId];
@@ -31,21 +81,75 @@ program
             : chalk.gray('not installed');
         console.log(`  ${agent.name.padEnd(14)} ${status}`);
     }
-    console.log(chalk.bold('\nInstalled Skills\n'));
+    console.log(chalk.bold('\nInstalled Commands\n'));
     for (const agentId of ALL_AGENT_IDS) {
         const agent = AGENTS[agentId];
-        const skills = listInstalledSkills(agentId);
+        const commands = listInstalledCommandsWithScope(agentId, cwd);
+        const userCommands = commands.filter((c) => c.scope === 'user');
+        const projectCommands = commands.filter((c) => c.scope === 'project');
+        if (commands.length > 0) {
+            const parts = [];
+            if (userCommands.length > 0) {
+                parts.push(`${chalk.cyan(userCommands.length)} user`);
+            }
+            if (projectCommands.length > 0) {
+                parts.push(`${chalk.yellow(projectCommands.length)} project`);
+            }
+            console.log(`  ${agent.name}: ${parts.join(', ')}`);
+        }
+    }
+    console.log(chalk.bold('\nInstalled Skills\n'));
+    for (const agentId of SKILLS_CAPABLE_AGENTS) {
+        const agent = AGENTS[agentId];
+        const skills = listInstalledSkillsWithScope(agentId, cwd);
+        const userSkills = skills.filter((s) => s.scope === 'user');
+        const projectSkills = skills.filter((s) => s.scope === 'project');
         if (skills.length > 0) {
-            console.log(`  ${agent.name}: ${chalk.cyan(skills.length)} skills`);
+            const parts = [];
+            if (userSkills.length > 0) {
+                parts.push(`${chalk.cyan(userSkills.length)} user`);
+            }
+            if (projectSkills.length > 0) {
+                parts.push(`${chalk.yellow(projectSkills.length)} project`);
+            }
+            console.log(`  ${agent.name}: ${parts.join(', ')}`);
+        }
+    }
+    console.log(chalk.bold('\nInstalled MCP Servers\n'));
+    for (const agentId of MCP_CAPABLE_AGENTS) {
+        const agent = AGENTS[agentId];
+        if (!isCliInstalled(agentId))
+            continue;
+        const mcps = listInstalledMcpsWithScope(agentId, cwd);
+        const userMcps = mcps.filter((m) => m.scope === 'user');
+        const projectMcps = mcps.filter((m) => m.scope === 'project');
+        if (mcps.length > 0) {
+            const parts = [];
+            if (userMcps.length > 0) {
+                parts.push(`${chalk.cyan(userMcps.length)} user`);
+            }
+            if (projectMcps.length > 0) {
+                parts.push(`${chalk.yellow(projectMcps.length)} project`);
+            }
+            console.log(`  ${agent.name}: ${parts.join(', ')}`);
         }
     }
-    if (state.source) {
-        console.log(chalk.bold('\nSync Source\n'));
-        console.log(`  ${state.source}`);
-        if (state.lastSync) {
-            console.log(`  Last sync: ${new Date(state.lastSync).toLocaleString()}`);
+    const scopes = getScopesByPriority();
+    if (scopes.length > 0) {
+        console.log(chalk.bold('\nConfigured Scopes\n'));
+        for (const { name, config } of scopes) {
+            const readonlyTag = config.readonly ? chalk.gray(' (readonly)') : '';
+            const priorityTag = chalk.gray(` [priority: ${config.priority}]`);
+            console.log(`  ${chalk.bold(name)}${readonlyTag}${priorityTag}`);
+            console.log(`    ${config.source}`);
+            console.log(`    Branch: ${config.branch}  Commit: ${config.commit.substring(0, 8)}`);
+            console.log(`    Last sync: ${new Date(config.lastSync).toLocaleString()}`);
         }
     }
+    else {
+        console.log(chalk.bold('\nNo scopes configured\n'));
+        console.log(chalk.gray('  Run: agents repo add <source>'));
+    }
     console.log();
 });
 // =============================================================================
@@ -56,18 +160,29 @@ program
     .description('Pull and sync from remote .agents repo')
     .option('-y, --yes', 'Skip interactive prompts')
     .option('-f, --force', 'Overwrite local changes')
+    .option('-s, --scope <scope>', 'Target scope (default: user)', 'user')
     .option('--dry-run', 'Show what would change')
     .option('--skip-clis', 'Skip CLI installation')
     .option('--skip-mcp', 'Skip MCP registration')
     .action(async (source, options) => {
-    const state = readState();
-    const targetSource = source || state.source;
+    const scopeName = options.scope;
+    const meta = readState();
+    const existingScope = meta.scopes[scopeName];
+    const targetSource = source || existingScope?.source;
     if (!targetSource) {
-        console.log(chalk.red('No source specified. Usage: agents pull <source>'));
+        console.log(chalk.red(`No source specified for scope '${scopeName}'.`));
+        const scopeHint = scopeName === 'user' ? '' : ` --scope ${scopeName}`;
+        console.log(chalk.gray(`  Usage: agents pull <source>${scopeHint}`));
         console.log(chalk.gray('  Example: agents pull gh:username/.agents'));
         process.exit(1);
     }
-    const spinner = ora('Cloning repository...').start();
+    // Prevent modification of readonly scopes
+    if (existingScope?.readonly && !options.force) {
+        console.log(chalk.red(`Scope '${scopeName}' is readonly. Use --force to override.`));
+        process.exit(1);
+    }
+    const parsed = parseSource(targetSource);
+    const spinner = ora(`Cloning repository for ${scopeName} scope...`).start();
     try {
         const { localPath, commit, isNew } = await cloneRepo(targetSource);
         spinner.succeed(isNew ? 'Repository cloned' : 'Repository updated');
@@ -75,14 +190,14 @@ program
         if (!manifest) {
             console.log(chalk.yellow(`No ${MANIFEST_FILENAME} found in repository`));
         }
-        const skills = discoverSkills(localPath);
-        console.log(chalk.bold(`\nFound ${skills.length} skills\n`));
-        for (const skill of skills.slice(0, 10)) {
-            const source = skill.isShared ? 'shared' : skill.agentSpecific;
-            console.log(`  ${chalk.cyan(skill.name.padEnd(20))} ${chalk.gray(source)}`);
+        const commands = discoverCommands(localPath);
+        console.log(chalk.bold(`\nFound ${commands.length} commands\n`));
+        for (const command of commands.slice(0, 10)) {
+            const src = command.isShared ? 'shared' : command.agentSpecific;
+            console.log(`  ${chalk.cyan(command.name.padEnd(20))} ${chalk.gray(src)}`);
         }
-        if (skills.length > 10) {
-            console.log(chalk.gray(`  ... and ${skills.length - 10} more`));
+        if (commands.length > 10) {
+            console.log(chalk.gray(`  ... and ${commands.length - 10} more`));
         }
         if (options.dryRun) {
             console.log(chalk.yellow('\nDry run - no changes made'));
@@ -114,20 +229,20 @@ program
             });
         }
         const defaultAgents = selectedAgents;
-        const installSpinner = ora('Installing skills...').start();
+        const installSpinner = ora('Installing commands...').start();
         let installed = 0;
-        for (const skill of skills) {
+        for (const command of commands) {
             for (const agentId of defaultAgents) {
                 if (!isCliInstalled(agentId) && agentId !== 'cursor')
                     continue;
-                const sourcePath = resolveSkillSource(localPath, skill.name, agentId);
+                const sourcePath = resolveCommandSource(localPath, command.name, agentId);
                 if (sourcePath) {
-                    installSkill(sourcePath, agentId, skill.name, method);
+                    installCommand(sourcePath, agentId, command.name, method);
                     installed++;
                 }
             }
         }
-        installSpinner.succeed(`Installed ${installed} skill instances`);
+        installSpinner.succeed(`Installed ${installed} command instances`);
         if (!options.skipMcp && manifest?.mcp) {
             const mcpSpinner = ora('Registering MCP servers...').start();
             let registered = 0;
@@ -144,12 +259,17 @@ program
             }
             mcpSpinner.succeed(`Registered ${registered} MCP servers`);
         }
-        writeState({
-            ...state,
+        // Update scope config
+        const priority = getScopePriority(scopeName);
+        setScope(scopeName, {
             source: targetSource,
+            branch: parsed.ref || 'main',
+            commit,
             lastSync: new Date().toISOString(),
+            priority,
+            readonly: scopeName === 'system',
         });
-        console.log(chalk.green('\nSync complete.'));
+        console.log(chalk.green(`\nSync complete. Updated scope: ${scopeName}`));
     }
     catch (err) {
         spinner.fail('Failed to sync');
@@ -162,15 +282,23 @@ program
 // =============================================================================
 program
     .command('push')
-    .description('Export local skills to .agents repo for manual commit')
-    .option('--export-only', 'Only export skills, do not update manifest')
+    .description('Export local configuration to .agents repo for manual commit')
+    .option('-s, --scope <scope>', 'Target scope (default: user)', 'user')
+    .option('--export-only', 'Only export, do not update manifest')
     .action(async (options) => {
-    const state = readState();
-    if (!state.source) {
-        console.log(chalk.red('No .agents repo configured. Run: agents pull <source>'));
+    const scopeName = options.scope;
+    const scope = getScope(scopeName);
+    if (!scope) {
+        console.log(chalk.red(`Scope '${scopeName}' not configured.`));
+        const scopeHint = scopeName === 'user' ? '' : ` --scope ${scopeName}`;
+        console.log(chalk.gray(`  Run: agents repo add <source>${scopeHint}`));
+        process.exit(1);
+    }
+    if (scope.readonly) {
+        console.log(chalk.red(`Scope '${scopeName}' is readonly. Cannot push.`));
         process.exit(1);
     }
-    const localPath = getRepoLocalPath(state.source);
+    const localPath = getRepoLocalPath(scope.source);
     const manifest = readManifest(localPath) || createDefaultManifest();
     console.log(chalk.bold('\nExporting local configuration...\n'));
     const cliStates = getAllCliStates();
@@ -218,71 +346,89 @@ program
     await program.commands.find((c) => c.name() === 'pull')?.parseAsync(args, { from: 'user' });
 });
 // =============================================================================
-// SKILLS COMMANDS
+// COMMANDS COMMANDS
 // =============================================================================
-const skillsCmd = program
-    .command('skills')
-    .description('Manage skills/commands');
-skillsCmd
+const commandsCmd = program
+    .command('commands')
+    .description('Manage slash commands');
+commandsCmd
     .command('list')
-    .description('List installed skills')
-    .option('-a, --agent <agent>', 'Show skills for specific agent')
+    .description('List installed commands')
+    .option('-a, --agent <agent>', 'Filter by agent')
+    .option('-s, --scope <scope>', 'Filter by scope: user, project, or all', 'all')
     .action((options) => {
-    console.log(chalk.bold('\nInstalled Skills\n'));
+    console.log(chalk.bold('\nInstalled Commands\n'));
+    const cwd = process.cwd();
     const agents = options.agent
         ? [options.agent]
         : ALL_AGENT_IDS;
     for (const agentId of agents) {
         const agent = AGENTS[agentId];
-        const skills = listInstalledSkills(agentId);
-        if (skills.length === 0) {
+        let commands = listInstalledCommandsWithScope(agentId, cwd);
+        if (options.scope !== 'all') {
+            commands = commands.filter((c) => c.scope === options.scope);
+        }
+        if (commands.length === 0) {
             console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('none')}`);
         }
         else {
             console.log(`  ${chalk.bold(agent.name)}:`);
-            for (const skill of skills) {
-                console.log(`    ${chalk.cyan(skill)}`);
+            const userCommands = commands.filter((c) => c.scope === 'user');
+            const projectCommands = commands.filter((c) => c.scope === 'project');
+            if (userCommands.length > 0 && (options.scope === 'all' || options.scope === 'user')) {
+                console.log(`    ${chalk.gray('User:')}`);
+                for (const cmd of userCommands) {
+                    const desc = cmd.description ? ` - ${chalk.gray(cmd.description)}` : '';
+                    console.log(`      ${chalk.cyan(cmd.name)}${desc}`);
+                }
+            }
+            if (projectCommands.length > 0 && (options.scope === 'all' || options.scope === 'project')) {
+                console.log(`    ${chalk.gray('Project:')}`);
+                for (const cmd of projectCommands) {
+                    const desc = cmd.description ? ` - ${chalk.gray(cmd.description)}` : '';
+                    console.log(`      ${chalk.yellow(cmd.name)}${desc}`);
+                }
             }
         }
         console.log();
     }
 });
-skillsCmd
+commandsCmd
     .command('add <source>')
-    .description('Add skill from Git repo or local path')
+    .description('Add commands from Git repo or local path')
     .option('-a, --agents <list>', 'Comma-separated agents to install to')
     .action(async (source, options) => {
-    const spinner = ora('Fetching skill...').start();
+    const spinner = ora('Fetching commands...').start();
     try {
         const { localPath } = await cloneRepo(source);
-        const skills = discoverSkills(localPath);
-        spinner.succeed(`Found ${skills.length} skills`);
+        const commands = discoverCommands(localPath);
+        spinner.succeed(`Found ${commands.length} commands`);
         const agents = options.agents
             ? options.agents.split(',')
             : ['claude', 'codex', 'gemini'];
-        for (const skill of skills) {
-            console.log(`\n  ${chalk.cyan(skill.name)}: ${skill.description}`);
+        for (const command of commands) {
+            console.log(`\n  ${chalk.cyan(command.name)}: ${command.description}`);
             for (const agentId of agents) {
                 if (!isCliInstalled(agentId) && agentId !== 'cursor')
                     continue;
-                const sourcePath = resolveSkillSource(localPath, skill.name, agentId);
+                const sourcePath = resolveCommandSource(localPath, command.name, agentId);
                 if (sourcePath) {
-                    installSkill(sourcePath, agentId, skill.name, 'symlink');
+                    installCommand(sourcePath, agentId, command.name, 'symlink');
                     console.log(`    ${chalk.green('+')} ${AGENTS[agentId].name}`);
                 }
             }
         }
-        console.log(chalk.green('\nSkills installed.'));
+        console.log(chalk.green('\nCommands installed.'));
     }
     catch (err) {
-        spinner.fail('Failed to add skill');
+        spinner.fail('Failed to add commands');
         console.error(chalk.red(err.message));
         process.exit(1);
     }
 });
-skillsCmd
+commandsCmd
     .command('remove <name>')
-    .description('Remove a skill from all agents')
+    .description('Remove a command from all agents')
     .option('-a, --agents <list>', 'Comma-separated agents to remove from')
     .action((name, options) => {
     const agents = options.agents
@@ -290,18 +436,389 @@ skillsCmd
         : ALL_AGENT_IDS;
     let removed = 0;
     for (const agentId of agents) {
-        if (uninstallSkill(agentId, name)) {
+        if (uninstallCommand(agentId, name)) {
             console.log(`  ${chalk.red('-')} ${AGENTS[agentId].name}`);
             removed++;
         }
     }
     if (removed === 0) {
-        console.log(chalk.yellow(`Skill '${name}' not found`));
+        console.log(chalk.yellow(`Command '${name}' not found`));
     }
     else {
         console.log(chalk.green(`\nRemoved from ${removed} agents.`));
     }
 });
+commandsCmd
+    .command('push <name>')
+    .description('Save project-scoped command to user scope')
+    .option('-a, --agents <list>', 'Comma-separated agents to push for')
+    .action((name, options) => {
+    const cwd = process.cwd();
+    const agents = options.agents
+        ? options.agents.split(',')
+        : ALL_AGENT_IDS;
+    let pushed = 0;
+    for (const agentId of agents) {
+        if (!isCliInstalled(agentId) && agentId !== 'cursor')
+            continue;
+        const result = promoteCommandToUser(agentId, name, cwd);
+        if (result.success) {
+            console.log(`  ${chalk.green('+')} ${AGENTS[agentId].name}`);
+            pushed++;
+        }
+        else if (result.error && !result.error.includes('not found')) {
+            console.log(`  ${chalk.red('x')} ${AGENTS[agentId].name}: ${result.error}`);
+        }
+    }
+    if (pushed === 0) {
+        console.log(chalk.yellow(`Project command '${name}' not found for any agent`));
+    }
+    else {
+        console.log(chalk.green(`\nPushed to user scope for ${pushed} agents.`));
+    }
+});
+const hooksCmd = program.command('hooks').description('Manage hooks');
+hooksCmd
+    .command('list')
+    .description('List installed hooks')
+    .option('-a, --agent <agent>', 'Filter by agent')
+    .option('-s, --scope <scope>', 'Filter by scope: user, project, or all', 'all')
+    .action((options) => {
+    console.log(chalk.bold('\nInstalled Hooks\n'));
+    const cwd = process.cwd();
+    const agents = options.agent
+        ? [options.agent]
+        : Array.from(HOOKS_CAPABLE_AGENTS);
+    for (const agentId of agents) {
+        const agent = AGENTS[agentId];
+        if (!agent.supportsHooks) {
+            console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('hooks not supported')}`);
+            console.log();
+            continue;
+        }
+        let hooks = listInstalledHooksWithScope(agentId, cwd);
+        if (options.scope !== 'all') {
+            hooks = hooks.filter((h) => h.scope === options.scope);
+        }
+        if (hooks.length === 0) {
+            console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('none')}`);
+        }
+        else {
+            console.log(`  ${chalk.bold(agent.name)}:`);
+            const userHooks = hooks.filter((h) => h.scope === 'user');
+            const projectHooks = hooks.filter((h) => h.scope === 'project');
+            if (userHooks.length > 0 && (options.scope === 'all' || options.scope === 'user')) {
+                console.log(`    ${chalk.gray('User:')}`);
+                for (const hook of userHooks) {
+                    console.log(`      ${chalk.cyan(hook.name)}`);
+                }
+            }
+            if (projectHooks.length > 0 && (options.scope === 'all' || options.scope === 'project')) {
+                console.log(`    ${chalk.gray('Project:')}`);
+                for (const hook of projectHooks) {
+                    console.log(`      ${chalk.yellow(hook.name)}`);
+                }
+            }
+        }
+        console.log();
+    }
+});
+hooksCmd
+    .command('add <source>')
+    .description('Install hooks from git repo or local path')
+    .option('-a, --agent <agents>', 'Target agents (comma-separated)', 'claude,gemini')
+    .action(async (source, options) => {
+    const spinner = ora('Fetching hooks...').start();
+    try {
+        const { localPath } = await cloneRepo(source);
+        const hooks = discoverHooksFromRepo(localPath);
+        const hookNames = new Set();
+        for (const name of hooks.shared) {
+            hookNames.add(name);
+        }
+        for (const list of Object.values(hooks.agentSpecific)) {
+            for (const name of list) {
+                hookNames.add(name);
+            }
+        }
+        spinner.succeed(`Found ${hookNames.size} hooks`);
+        const agents = options.agent
+            ? options.agent.split(',')
+            : ['claude', 'gemini'];
+        const result = await installHooks(localPath, agents, { scope: 'user' });
+        const installedByHook = new Map();
+        for (const item of result.installed) {
+            const [name, agentId] = item.split(':');
+            const list = installedByHook.get(name) || [];
+            list.push(agentId);
+            installedByHook.set(name, list);
+        }
+        const orderedHooks = Array.from(installedByHook.keys()).sort((a, b) => a.localeCompare(b));
+        for (const name of orderedHooks) {
+            console.log(`\n  ${chalk.cyan(name)}`);
+            const agentIds = installedByHook.get(name) || [];
+            agentIds.sort();
+            for (const agentId of agentIds) {
+                console.log(`    ${AGENTS[agentId].name}`);
+            }
+        }
+        if (result.errors.length > 0) {
+            console.log(chalk.red('\nErrors:'));
+            for (const error of result.errors) {
+                console.log(chalk.red(`  ${error}`));
+            }
+        }
+        if (result.installed.length === 0) {
+            console.log(chalk.yellow('\nNo hooks installed.'));
+        }
+        else {
+            console.log(chalk.green('\nHooks installed.'));
+        }
+    }
+    catch (err) {
+        spinner.fail('Failed to add hooks');
+        console.error(chalk.red(err.message));
+        process.exit(1);
+    }
+});
+hooksCmd
+    .command('remove <name>')
+    .description('Remove a hook')
+    .option('-a, --agent <agents>', 'Target agents (comma-separated)')
+    .action(async (name, options) => {
+    const agents = options.agent
+        ? options.agent.split(',')
+        : Array.from(HOOKS_CAPABLE_AGENTS);
+    const result = await removeHook(name, agents);
+    let removed = 0;
+    for (const item of result.removed) {
+        const [, agentId] = item.split(':');
+        console.log(`  ${AGENTS[agentId].name}`);
+        removed++;
+    }
+    if (result.errors.length > 0) {
+        console.log(chalk.red('\nErrors:'));
+        for (const error of result.errors) {
+            console.log(chalk.red(`  ${error}`));
+        }
+    }
+    if (removed === 0) {
+        console.log(chalk.yellow(`Hook '${name}' not found`));
+    }
+    else {
+        console.log(chalk.green(`\nRemoved from ${removed} agents.`));
+    }
+});
+hooksCmd
+    .command('push <name>')
+    .description('Copy project-scoped hook to user scope')
+    .option('-a, --agent <agents>', 'Target agents (comma-separated)')
+    .action((name, options) => {
+    const cwd = process.cwd();
+    const agents = options.agent
+        ? options.agent.split(',')
+        : Array.from(HOOKS_CAPABLE_AGENTS);
+    let pushed = 0;
+    for (const agentId of agents) {
+        const result = promoteHookToUser(agentId, name, cwd);
+        if (result.success) {
+            console.log(`  ${AGENTS[agentId].name}`);
+            pushed++;
+        }
+        else if (result.error && !result.error.includes('not found')) {
+            console.log(`  ${AGENTS[agentId].name}: ${result.error}`);
+        }
+    }
+    if (pushed === 0) {
+        console.log(chalk.yellow(`Project hook '${name}' not found for any agent`));
+    }
+    else {
+        console.log(chalk.green(`\nPushed to user scope for ${pushed} agents.`));
+    }
+});
+// =============================================================================
+// SKILLS COMMANDS (Agent Skills)
+// =============================================================================
+const skillsCmd = program
+    .command('skills')
+    .description('Manage Agent Skills (SKILL.md + rules/)');
+skillsCmd
+    .command('list')
+    .description('List installed Agent Skills')
+    .option('-a, --agent <agent>', 'Filter by agent')
+    .option('-s, --scope <scope>', 'Filter by scope: user, project, or all', 'all')
+    .action((options) => {
+    console.log(chalk.bold('\nInstalled Agent Skills\n'));
+    const cwd = process.cwd();
+    const agents = options.agent
+        ? [options.agent]
+        : SKILLS_CAPABLE_AGENTS;
+    for (const agentId of agents) {
+        const agent = AGENTS[agentId];
+        if (!agent.capabilities.skills) {
+            console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('skills not supported')}`);
+            console.log();
+            continue;
+        }
+        let skills = listInstalledSkillsWithScope(agentId, cwd);
+        if (options.scope !== 'all') {
+            skills = skills.filter((s) => s.scope === options.scope);
+        }
+        if (skills.length === 0) {
+            console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('none')}`);
+        }
+        else {
+            console.log(`  ${chalk.bold(agent.name)}:`);
+            const userSkills = skills.filter((s) => s.scope === 'user');
+            const projectSkills = skills.filter((s) => s.scope === 'project');
+            if (userSkills.length > 0 && (options.scope === 'all' || options.scope === 'user')) {
+                console.log(`    ${chalk.gray('User:')}`);
+                for (const skill of userSkills) {
+                    const desc = skill.metadata.description ? ` - ${chalk.gray(skill.metadata.description)}` : '';
+                    const ruleInfo = skill.ruleCount > 0 ? chalk.gray(` (${skill.ruleCount} rules)`) : '';
+                    console.log(`      ${chalk.cyan(skill.name)}${desc}${ruleInfo}`);
+                }
+            }
+            if (projectSkills.length > 0 && (options.scope === 'all' || options.scope === 'project')) {
+                console.log(`    ${chalk.gray('Project:')}`);
+                for (const skill of projectSkills) {
+                    const desc = skill.metadata.description ? ` - ${chalk.gray(skill.metadata.description)}` : '';
+                    const ruleInfo = skill.ruleCount > 0 ? chalk.gray(` (${skill.ruleCount} rules)`) : '';
+                    console.log(`      ${chalk.yellow(skill.name)}${desc}${ruleInfo}`);
+                }
+            }
+        }
+        console.log();
+    }
+});
+skillsCmd
+    .command('add <source>')
+    .description('Add Agent Skills from Git repo or local path')
+    .option('-a, --agents <list>', 'Comma-separated agents to install to')
+    .action(async (source, options) => {
+    const spinner = ora('Fetching skills...').start();
+    try {
+        const { localPath } = await cloneRepo(source);
+        const skills = discoverSkillsFromRepo(localPath);
+        spinner.succeed(`Found ${skills.length} skills`);
+        if (skills.length === 0) {
+            console.log(chalk.yellow('No skills found (looking for SKILL.md files)'));
+            return;
+        }
+        for (const skill of skills) {
+            console.log(`\n  ${chalk.cyan(skill.name)}: ${skill.metadata.description || 'no description'}`);
+            if (skill.ruleCount > 0) {
+                console.log(`    ${chalk.gray(`${skill.ruleCount} rules`)}`);
+            }
+        }
+        const agents = options.agents
+            ? options.agents.split(',')
+            : await checkbox({
+                message: 'Select agents to install skills to:',
+                choices: SKILLS_CAPABLE_AGENTS.filter((id) => isCliInstalled(id) || id === 'cursor').map((id) => ({
+                    name: AGENTS[id].name,
+                    value: id,
+                    checked: ['claude', 'codex', 'gemini'].includes(id),
+                })),
+            });
+        if (agents.length === 0) {
+            console.log(chalk.yellow('\nNo agents selected.'));
+            return;
+        }
+        const installSpinner = ora('Installing skills...').start();
+        let installed = 0;
+        for (const skill of skills) {
+            const result = installSkill(skill.path, skill.name, agents);
+            if (result.success) {
+                installed++;
+            }
+            else {
+                console.log(chalk.red(`\n  Failed to install ${skill.name}: ${result.error}`));
+            }
+        }
+        installSpinner.succeed(`Installed ${installed} skills to ${agents.length} agents`);
+        console.log(chalk.green('\nSkills installed.'));
+    }
+    catch (err) {
+        spinner.fail('Failed to add skills');
+        console.error(chalk.red(err.message));
+        process.exit(1);
+    }
+});
+skillsCmd
+    .command('remove <name>')
+    .description('Remove an Agent Skill')
+    .action((name) => {
+    const result = uninstallSkill(name);
+    if (result.success) {
+        console.log(chalk.green(`Removed skill '${name}'`));
+    }
+    else {
+        console.log(chalk.red(result.error || 'Failed to remove skill'));
+    }
+});
+skillsCmd
+    .command('push <name>')
+    .description('Save project-scoped skill to user scope')
+    .option('-a, --agents <list>', 'Comma-separated agents to push for')
+    .action((name, options) => {
+    const cwd = process.cwd();
+    const agents = options.agents
+        ? options.agents.split(',')
+        : SKILLS_CAPABLE_AGENTS;
+    let pushed = 0;
+    for (const agentId of agents) {
+        if (!AGENTS[agentId].capabilities.skills)
+            continue;
+        const result = promoteSkillToUser(agentId, name, cwd);
+        if (result.success) {
+            console.log(`  ${chalk.green('+')} ${AGENTS[agentId].name}`);
+            pushed++;
+        }
+        else if (result.error && !result.error.includes('not found')) {
+            console.log(`  ${chalk.red('x')} ${AGENTS[agentId].name}: ${result.error}`);
+        }
+    }
+    if (pushed === 0) {
+        console.log(chalk.yellow(`Project skill '${name}' not found for any agent`));
+    }
+    else {
+        console.log(chalk.green(`\nPushed to user scope for ${pushed} agents.`));
+    }
+});
+skillsCmd
+    .command('info <name>')
+    .description('Show detailed info about an installed skill')
+    .action((name) => {
+    const skill = getSkillInfo(name);
+    if (!skill) {
+        console.log(chalk.yellow(`Skill '${name}' not found`));
+        return;
+    }
+    console.log(chalk.bold(`\n${skill.metadata.name}\n`));
+    if (skill.metadata.description) {
+        console.log(`  ${skill.metadata.description}`);
+    }
+    console.log();
+    if (skill.metadata.author) {
+        console.log(`  Author: ${skill.metadata.author}`);
+    }
+    if (skill.metadata.version) {
+        console.log(`  Version: ${skill.metadata.version}`);
+    }
+    if (skill.metadata.license) {
+        console.log(`  License: ${skill.metadata.license}`);
+    }
+    console.log(`  Path: ${skill.path}`);
+    const rules = getSkillRules(name);
+    if (rules.length > 0) {
+        console.log(chalk.bold(`\n  Rules (${rules.length}):\n`));
+        for (const rule of rules) {
+            console.log(`    ${chalk.cyan(rule)}`);
+        }
+    }
+    console.log();
+});
 // =============================================================================
 // MCP COMMANDS
 // =============================================================================
@@ -311,32 +828,71 @@ const mcpCmd = program
 mcpCmd
     .command('list')
     .description('List MCP servers and registration status')
-    .action(() => {
+    .option('-a, --agent <agent>', 'Filter by agent')
+    .option('-s, --scope <scope>', 'Filter by scope: user, project, or all', 'all')
+    .action((options) => {
     console.log(chalk.bold('\nMCP Servers\n'));
-    for (const agentId of MCP_CAPABLE_AGENTS) {
+    const cwd = process.cwd();
+    const agents = options.agent
+        ? [options.agent]
+        : MCP_CAPABLE_AGENTS;
+    for (const agentId of agents) {
         const agent = AGENTS[agentId];
+        if (!agent.capabilities.mcp) {
+            console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('mcp not supported')}`);
+            console.log();
+            continue;
+        }
         if (!isCliInstalled(agentId)) {
             console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('CLI not installed')}`);
             continue;
         }
-        console.log(`  ${chalk.bold(agent.name)}:`);
-        const swarmRegistered = isMcpRegistered(agentId, 'Swarm');
-        console.log(`    Swarm: ${swarmRegistered ? chalk.green('registered') : chalk.gray('not registered')}`);
+        let mcps = listInstalledMcpsWithScope(agentId, cwd);
+        if (options.scope !== 'all') {
+            mcps = mcps.filter((m) => m.scope === options.scope);
+        }
+        if (mcps.length === 0) {
+            console.log(`  ${chalk.bold(agent.name)}: ${chalk.gray('none')}`);
+        }
+        else {
+            console.log(`  ${chalk.bold(agent.name)}:`);
+            const userMcps = mcps.filter((m) => m.scope === 'user');
+            const projectMcps = mcps.filter((m) => m.scope === 'project');
+            if (userMcps.length > 0 && (options.scope === 'all' || options.scope === 'user')) {
+                console.log(`    ${chalk.gray('User:')}`);
+                for (const mcp of userMcps) {
+                    console.log(`      ${chalk.cyan(mcp.name)}`);
+                }
+            }
+            if (projectMcps.length > 0 && (options.scope === 'all' || options.scope === 'project')) {
+                console.log(`    ${chalk.gray('Project:')}`);
+                for (const mcp of projectMcps) {
+                    console.log(`      ${chalk.yellow(mcp.name)}`);
+                }
+            }
+        }
         console.log();
     }
 });
 mcpCmd
-    .command('add <name> <command>')
-    .description('Add MCP server to manifest')
+    .command('add <name>')
+    .description('Add MCP server to manifest (use -- before command)')
     .option('-a, --agents <list>', 'Comma-separated agents', 'claude,codex,gemini')
     .option('-s, --scope <scope>', 'Scope: user or project', 'user')
-    .action((name, command, options) => {
-    const state = readState();
-    if (!state.source) {
-        console.log(chalk.yellow('No .agents repo configured. Run: agents pull <source>'));
-        return;
+    .allowUnknownOption(true)
+    .action(async (name, options, cmd) => {
+    // Get everything after -- as the command
+    const rawArgs = cmd.args || [];
+    const commandParts = rawArgs.slice(rawArgs.indexOf(name) + 1);
+    if (commandParts.length === 0) {
+        console.error(chalk.red('Error: Command required after --'));
+        console.log(chalk.gray('Usage: agents mcp add <name> -- <command...>'));
+        console.log(chalk.gray('Example: agents mcp add swarm -- npx @swarmify/agents-mcp'));
+        process.exit(1);
     }
-    const localPath = getRepoLocalPath(state.source);
+    const command = commandParts.join(' ');
+    const source = await ensureSource();
+    const localPath = getRepoLocalPath(source);
     const manifest = readManifest(localPath) || createDefaultManifest();
     manifest.mcp = manifest.mcp || {};
     manifest.mcp[name] = {
@@ -378,14 +934,10 @@ mcpCmd
     .command('register [name]')
     .description('Register MCP server(s) with agent CLIs')
     .option('-a, --agents <list>', 'Comma-separated agents')
-    .action((name, options) => {
-    const state = readState();
+    .action(async (name, options) => {
     if (!name) {
-        if (!state.source) {
-            console.log(chalk.yellow('No .agents repo configured. Run: agents pull <source>'));
-            return;
-        }
-        const localPath = getRepoLocalPath(state.source);
+        const source = await ensureSource();
+        const localPath = getRepoLocalPath(source);
         const manifest = readManifest(localPath);
         if (!manifest?.mcp) {
             console.log(chalk.yellow('No MCP servers in manifest'));
@@ -409,6 +961,35 @@ mcpCmd
     }
     console.log(chalk.yellow('Single MCP registration not yet implemented'));
 });
+mcpCmd
+    .command('push <name>')
+    .description('Save project-scoped MCP to user scope')
+    .option('-a, --agents <list>', 'Comma-separated agents to push for')
+    .action((name, options) => {
+    const cwd = process.cwd();
+    const agents = options.agents
+        ? options.agents.split(',')
+        : MCP_CAPABLE_AGENTS;
+    let pushed = 0;
+    for (const agentId of agents) {
+        if (!isCliInstalled(agentId))
+            continue;
+        const result = promoteMcpToUser(agentId, name, cwd);
+        if (result.success) {
+            console.log(`  ${chalk.green('+')} ${AGENTS[agentId].name}`);
+            pushed++;
+        }
+        else if (result.error && !result.error.includes('not found')) {
+            console.log(`  ${chalk.red('x')} ${AGENTS[agentId].name}: ${result.error}`);
+        }
+    }
+    if (pushed === 0) {
+        console.log(chalk.yellow(`Project MCP '${name}' not found for any agent`));
+    }
+    else {
+        console.log(chalk.green(`\nPushed to user scope for ${pushed} agents.`));
+    }
+});
 // =============================================================================
 // CLI COMMANDS
 // =============================================================================
@@ -440,19 +1021,15 @@ cliCmd
     .command('add <agent>')
     .description('Add agent CLI to manifest')
     .option('-v, --version <version>', 'Version to pin', 'latest')
-    .action((agent, options) => {
-    const state = readState();
-    if (!state.source) {
-        console.log(chalk.yellow('No .agents repo configured. Run: agents pull <source>'));
-        return;
-    }
+    .action(async (agent, options) => {
     const agentId = agent.toLowerCase();
     if (!AGENTS[agentId]) {
         console.log(chalk.red(`Unknown agent: ${agent}`));
         console.log(chalk.gray(`Available: ${ALL_AGENT_IDS.join(', ')}`));
         return;
     }
-    const localPath = getRepoLocalPath(state.source);
+    const source = await ensureSource();
+    const localPath = getRepoLocalPath(source);
     const manifest = readManifest(localPath) || createDefaultManifest();
     manifest.clis = manifest.clis || {};
     manifest.clis[agentId] = {
@@ -465,14 +1042,10 @@ cliCmd
 cliCmd
     .command('remove <agent>')
     .description('Remove agent CLI from manifest')
-    .action((agent) => {
-    const state = readState();
-    if (!state.source) {
-        console.log(chalk.yellow('No .agents repo configured. Run: agents pull <source>'));
-        return;
-    }
+    .action(async (agent) => {
+    const source = await ensureSource();
     const agentId = agent.toLowerCase();
-    const localPath = getRepoLocalPath(state.source);
+    const localPath = getRepoLocalPath(source);
     const manifest = readManifest(localPath);
     if (manifest?.clis?.[agentId]) {
         delete manifest.clis[agentId];
@@ -486,10 +1059,12 @@ cliCmd
 cliCmd
     .command('upgrade [agent]')
     .description('Upgrade agent CLI(s) to version in manifest')
+    .option('-s, --scope <scope>', 'Target scope (default: user)', 'user')
     .option('--latest', 'Upgrade to latest version (ignore manifest)')
     .action(async (agent, options) => {
-    const state = readState();
-    const localPath = state.source ? getRepoLocalPath(state.source) : null;
+    const scopeName = options.scope;
+    const scope = getScope(scopeName);
+    const localPath = scope ? getRepoLocalPath(scope.source) : null;
     const manifest = localPath ? readManifest(localPath) : null;
     const agentsToUpgrade = agent
         ? [agent.toLowerCase()]
@@ -520,6 +1095,145 @@ cliCmd
     }
 });
 // =============================================================================
+// REPO COMMANDS
+// =============================================================================
+const repoCmd = program
+    .command('repo')
+    .description('Manage .agents repository scopes');
+repoCmd
+    .command('list')
+    .description('List configured repository scopes')
+    .action(() => {
+    const scopes = getScopesByPriority();
+    if (scopes.length === 0) {
+        console.log(chalk.yellow('\nNo scopes configured.'));
+        console.log(chalk.gray('  Run: agents repo add <source>'));
+        console.log();
+        return;
+    }
+    console.log(chalk.bold('\nConfigured Scopes\n'));
+    console.log(chalk.gray('  Scopes are applied in priority order (higher overrides lower)\n'));
+    for (const { name, config } of scopes) {
+        const readonlyTag = config.readonly ? chalk.gray(' (readonly)') : '';
+        console.log(`  ${chalk.bold(name)}${readonlyTag}`);
+        console.log(`    Source:   ${config.source}`);
+        console.log(`    Branch:   ${config.branch}`);
+        console.log(`    Commit:   ${config.commit.substring(0, 8)}`);
+        console.log(`    Priority: ${config.priority}`);
+        console.log(`    Synced:   ${new Date(config.lastSync).toLocaleString()}`);
+        console.log();
+    }
+});
+repoCmd
+    .command('add <source>')
+    .description('Add a repository scope')
+    .option('-s, --scope <scope>', 'Target scope (default: user)', 'user')
+    .option('-y, --yes', 'Skip confirmation prompts')
+    .action(async (source, options) => {
+    const scopeName = options.scope;
+    const existingScope = getScope(scopeName);
+    if (existingScope && !options.yes) {
+        const shouldOverwrite = await confirm({
+            message: `Scope '${scopeName}' already exists (${existingScope.source}). Overwrite?`,
+            default: false,
+        });
+        if (!shouldOverwrite) {
+            console.log(chalk.yellow('Cancelled.'));
+            return;
+        }
+    }
+    if (existingScope?.readonly && !options.yes) {
+        console.log(chalk.red(`Scope '${scopeName}' is readonly. Cannot overwrite.`));
+        return;
+    }
+    const parsed = parseSource(source);
+    const spinner = ora(`Cloning repository for ${scopeName} scope...`).start();
+    try {
+        const { commit, isNew } = await cloneRepo(source);
+        spinner.succeed(isNew ? 'Repository cloned' : 'Repository updated');
+        const priority = getScopePriority(scopeName);
+        setScope(scopeName, {
+            source,
+            branch: parsed.ref || 'main',
+            commit,
+            lastSync: new Date().toISOString(),
+            priority,
+            readonly: scopeName === 'system',
+        });
+        console.log(chalk.green(`\nAdded scope '${scopeName}' with priority ${priority}`));
+        const scopeHint = scopeName === 'user' ? '' : ` --scope ${scopeName}`;
+        console.log(chalk.gray(`  Run: agents pull${scopeHint} to sync commands`));
+    }
+    catch (err) {
+        spinner.fail('Failed to add scope');
+        console.error(chalk.red(err.message));
+        process.exit(1);
+    }
+});
+repoCmd
+    .command('remove <scope>')
+    .description('Remove a repository scope')
+    .option('-y, --yes', 'Skip confirmation prompts')
+    .action(async (scopeName, options) => {
+    const existingScope = getScope(scopeName);
+    if (!existingScope) {
+        console.log(chalk.yellow(`Scope '${scopeName}' not found.`));
+        return;
+    }
+    if (existingScope.readonly) {
+        console.log(chalk.red(`Scope '${scopeName}' is readonly. Cannot remove.`));
+        return;
+    }
+    if (!options.yes) {
+        const shouldRemove = await confirm({
+            message: `Remove scope '${scopeName}' (${existingScope.source})?`,
+            default: false,
+        });
+        if (!shouldRemove) {
+            console.log(chalk.yellow('Cancelled.'));
+            return;
+        }
+    }
+    const removed = removeScope(scopeName);
+    if (removed) {
+        console.log(chalk.green(`Removed scope '${scopeName}'`));
+    }
+    else {
+        console.log(chalk.yellow(`Failed to remove scope '${scopeName}'`));
+    }
+});
+repoCmd
+    .command('sync [scope]')
+    .description('Sync a specific scope or all scopes')
+    .option('-y, --yes', 'Skip confirmation prompts')
+    .action(async (scopeName, options) => {
+    const scopes = scopeName ? [{ name: scopeName, config: getScope(scopeName) }].filter(s => s.config) : getScopesByPriority();
+    if (scopes.length === 0) {
+        console.log(chalk.yellow('No scopes to sync.'));
+        return;
+    }
+    for (const { name, config } of scopes) {
+        if (!config)
+            continue;
+        console.log(chalk.bold(`\nSyncing scope: ${name}`));
+        const spinner = ora('Updating repository...').start();
+        try {
+            const { commit } = await cloneRepo(config.source);
+            spinner.succeed('Repository updated');
+            setScope(name, {
+                ...config,
+                commit,
+                lastSync: new Date().toISOString(),
+            });
+        }
+        catch (err) {
+            spinner.fail(`Failed to sync ${name}`);
+            console.error(chalk.gray(err.message));
+        }
+    }
+    console.log(chalk.green('\nSync complete.'));
+});
+// =============================================================================
 // INIT COMMAND
 // =============================================================================
 program
@@ -544,5 +1258,341 @@ program
     console.log(chalk.gray('    claude/hooks/'));
     console.log();
 });
+// =============================================================================
+// REGISTRY COMMANDS
+// =============================================================================
+const registryCmd = program
+    .command('registry')
+    .description('Manage package registries (MCP servers, skills)');
+registryCmd
+    .command('list')
+    .description('List configured registries')
+    .option('-t, --type <type>', 'Filter by type: mcp or skill')
+    .action((options) => {
+    const types = options.type ? [options.type] : ['mcp', 'skill'];
+    console.log(chalk.bold('\nConfigured Registries\n'));
+    for (const type of types) {
+        console.log(chalk.bold(`  ${type.toUpperCase()}`));
+        const registries = getRegistries(type);
+        const entries = Object.entries(registries);
+        if (entries.length === 0) {
+            console.log(chalk.gray('    No registries configured'));
+        }
+        else {
+            for (const [name, config] of entries) {
+                const status = config.enabled ? chalk.green('enabled') : chalk.gray('disabled');
+                const isDefault = DEFAULT_REGISTRIES[type]?.[name] ? chalk.gray(' (default)') : '';
+                console.log(`    ${name}${isDefault}: ${status}`);
+                console.log(chalk.gray(`      ${config.url}`));
+            }
+        }
+        console.log();
+    }
+});
+registryCmd
+    .command('add <type> <name> <url>')
+    .description('Add a registry (type: mcp or skill)')
+    .option('--api-key <key>', 'API key for authentication')
+    .action((type, name, url, options) => {
+    if (type !== 'mcp' && type !== 'skill') {
+        console.log(chalk.red(`Invalid type '${type}'. Use 'mcp' or 'skill'.`));
+        process.exit(1);
+    }
+    setRegistry(type, name, {
+        url,
+        enabled: true,
+        apiKey: options.apiKey,
+    });
+    console.log(chalk.green(`Added ${type} registry '${name}'`));
+});
+registryCmd
+    .command('remove <type> <name>')
+    .description('Remove a registry')
+    .action((type, name) => {
+    if (type !== 'mcp' && type !== 'skill') {
+        console.log(chalk.red(`Invalid type '${type}'. Use 'mcp' or 'skill'.`));
+        process.exit(1);
+    }
+    // Check if it's a default registry
+    if (DEFAULT_REGISTRIES[type]?.[name]) {
+        console.log(chalk.yellow(`Cannot remove default registry '${name}'. Use 'agents registry disable' instead.`));
+        process.exit(1);
+    }
+    if (removeRegistry(type, name)) {
+        console.log(chalk.green(`Removed ${type} registry '${name}'`));
+    }
+    else {
+        console.log(chalk.yellow(`Registry '${name}' not found`));
+    }
+});
+registryCmd
+    .command('enable <type> <name>')
+    .description('Enable a registry')
+    .action((type, name) => {
+    if (type !== 'mcp' && type !== 'skill') {
+        console.log(chalk.red(`Invalid type '${type}'. Use 'mcp' or 'skill'.`));
+        process.exit(1);
+    }
+    const registries = getRegistries(type);
+    if (!registries[name]) {
+        console.log(chalk.yellow(`Registry '${name}' not found`));
+        process.exit(1);
+    }
+    setRegistry(type, name, { enabled: true });
+    console.log(chalk.green(`Enabled ${type} registry '${name}'`));
+});
+registryCmd
+    .command('disable <type> <name>')
+    .description('Disable a registry')
+    .action((type, name) => {
+    if (type !== 'mcp' && type !== 'skill') {
+        console.log(chalk.red(`Invalid type '${type}'. Use 'mcp' or 'skill'.`));
+        process.exit(1);
+    }
+    const registries = getRegistries(type);
+    if (!registries[name]) {
+        console.log(chalk.yellow(`Registry '${name}' not found`));
+        process.exit(1);
+    }
+    setRegistry(type, name, { enabled: false });
+    console.log(chalk.green(`Disabled ${type} registry '${name}'`));
+});
+registryCmd
+    .command('config <type> <name>')
+    .description('Configure a registry')
+    .option('--api-key <key>', 'Set API key')
+    .option('--url <url>', 'Update URL')
+    .action((type, name, options) => {
+    if (type !== 'mcp' && type !== 'skill') {
+        console.log(chalk.red(`Invalid type '${type}'. Use 'mcp' or 'skill'.`));
+        process.exit(1);
+    }
+    const registries = getRegistries(type);
+    if (!registries[name]) {
+        console.log(chalk.yellow(`Registry '${name}' not found`));
+        process.exit(1);
+    }
+    const updates = {};
+    if (options.apiKey)
+        updates.apiKey = options.apiKey;
+    if (options.url)
+        updates.url = options.url;
+    if (Object.keys(updates).length === 0) {
+        console.log(chalk.yellow('No options provided. Use --api-key or --url.'));
+        process.exit(1);
+    }
+    setRegistry(type, name, updates);
+    console.log(chalk.green(`Updated ${type} registry '${name}'`));
+});
+// =============================================================================
+// SEARCH COMMAND
+// =============================================================================
+program
+    .command('search <query>')
+    .description('Search registries for packages (MCP servers, skills)')
+    .option('-t, --type <type>', 'Filter by type: mcp or skill')
+    .option('-r, --registry <name>', 'Search specific registry')
+    .option('-l, --limit <n>', 'Max results', '20')
+    .action(async (query, options) => {
+    const spinner = ora('Searching registries...').start();
+    try {
+        const results = await searchRegistries(query, {
+            type: options.type,
+            registry: options.registry,
+            limit: parseInt(options.limit, 10),
+        });
+        spinner.stop();
+        if (results.length === 0) {
+            console.log(chalk.yellow('\nNo packages found.'));
+            if (!options.type) {
+                console.log(chalk.gray('\nTip: skill registries not yet available. Use gh:user/repo for skills.'));
+            }
+            return;
+        }
+        console.log(chalk.bold(`\nFound ${results.length} packages\n`));
+        // Group by type
+        const mcpResults = results.filter((r) => r.type === 'mcp');
+        const skillResults = results.filter((r) => r.type === 'skill');
+        if (mcpResults.length > 0) {
+            console.log(chalk.bold('  MCP Servers'));
+            for (const result of mcpResults) {
+                const desc = result.description
+                    ? chalk.gray(` - ${result.description.slice(0, 50)}${result.description.length > 50 ? '...' : ''}`)
+                    : '';
+                console.log(`    ${chalk.cyan(result.name)}${desc}`);
+                console.log(chalk.gray(`      Registry: ${result.registry}  Install: agents add mcp:${result.name}`));
+            }
+            console.log();
+        }
+        if (skillResults.length > 0) {
+            console.log(chalk.bold('  Skills'));
+            for (const result of skillResults) {
+                const desc = result.description
+                    ? chalk.gray(` - ${result.description.slice(0, 50)}${result.description.length > 50 ? '...' : ''}`)
+                    : '';
+                console.log(`    ${chalk.cyan(result.name)}${desc}`);
+                console.log(chalk.gray(`      Registry: ${result.registry}  Install: agents add skill:${result.name}`));
+            }
+            console.log();
+        }
+    }
+    catch (err) {
+        spinner.fail('Search failed');
+        console.error(chalk.red(err.message));
+        process.exit(1);
+    }
+});
+// =============================================================================
+// ADD COMMAND (unified package installation)
+// =============================================================================
+program
+    .command('add <identifier>')
+    .description('Add a package (mcp:name, skill:user/repo, or gh:user/repo)')
+    .option('-a, --agents <list>', 'Comma-separated agents to install to')
+    .action(async (identifier, options) => {
+    const spinner = ora('Resolving package...').start();
+    try {
+        const resolved = await resolvePackage(identifier);
+        if (!resolved) {
+            spinner.fail('Package not found');
+            console.log(chalk.gray('\nTip: Use explicit prefix (mcp:, skill:, gh:) or check the identifier.'));
+            process.exit(1);
+        }
+        spinner.succeed(`Found ${resolved.type} package`);
+        if (resolved.type === 'mcp') {
+            // Install MCP server
+            const entry = resolved.mcpEntry;
+            if (!entry) {
+                console.log(chalk.red('Failed to get MCP server details'));
+                process.exit(1);
+            }
+            console.log(chalk.bold(`\n${entry.name}`));
+            if (entry.description) {
+                console.log(chalk.gray(`  ${entry.description}`));
+            }
+            if (entry.repository?.url) {
+                console.log(chalk.gray(`  ${entry.repository.url}`));
+            }
+            // Get package info
+            const pkg = entry.packages?.[0];
+            if (!pkg) {
+                console.log(chalk.yellow('\nNo installable package found for this server.'));
+                console.log(chalk.gray('You may need to install it manually.'));
+                process.exit(1);
+            }
+            console.log(chalk.bold('\nPackage:'));
+            console.log(`  Name: ${pkg.name || pkg.registry_name}`);
+            console.log(`  Runtime: ${pkg.runtime || 'unknown'}`);
+            console.log(`  Transport: ${pkg.transport || 'stdio'}`);
+            if (pkg.packageArguments && pkg.packageArguments.length > 0) {
+                console.log(chalk.bold('\nRequired arguments:'));
+                for (const arg of pkg.packageArguments) {
+                    const req = arg.required ? chalk.red('*') : '';
+                    console.log(`  ${arg.name}${req}: ${arg.description || ''}`);
+                }
+            }
+            // Determine command based on runtime
+            let command;
+            if (pkg.runtime === 'node') {
+                command = `npx -y ${pkg.name || pkg.registry_name}`;
+            }
+            else if (pkg.runtime === 'python') {
+                command = `uvx ${pkg.name || pkg.registry_name}`;
+            }
+            else {
+                command = pkg.name || pkg.registry_name;
+            }
+            const agents = options.agents
+                ? options.agents.split(',')
+                : MCP_CAPABLE_AGENTS.filter((id) => isCliInstalled(id));
+            if (agents.length === 0) {
+                console.log(chalk.yellow('\nNo MCP-capable agents installed.'));
+                process.exit(1);
+            }
+            console.log(chalk.bold('\nInstalling to agents...'));
+            for (const agentId of agents) {
+                if (!isCliInstalled(agentId))
+                    continue;
+                const result = registerMcp(agentId, entry.name, command, 'user');
+                if (result.success) {
+                    console.log(`  ${chalk.green('+')} ${AGENTS[agentId].name}`);
+                }
+                else {
+                    console.log(`  ${chalk.red('x')} ${AGENTS[agentId].name}: ${result.error}`);
+                }
+            }
+            console.log(chalk.green('\nMCP server installed.'));
+        }
+        else if (resolved.type === 'git' || resolved.type === 'skill') {
+            // Install from git source (skills/commands/hooks)
+            console.log(chalk.bold(`\nInstalling from ${resolved.source}`));
+            const { localPath } = await cloneRepo(resolved.source);
+            // Discover what's in the repo
+            const commands = discoverCommands(localPath);
+            const skills = discoverSkillsFromRepo(localPath);
+            const hooks = discoverHooksFromRepo(localPath);
+            const hasCommands = commands.length > 0;
+            const hasSkills = skills.length > 0;
+            const hasHooks = hooks.shared.length > 0 || Object.values(hooks.agentSpecific).some((h) => h.length > 0);
+            if (!hasCommands && !hasSkills && !hasHooks) {
+                console.log(chalk.yellow('No installable content found in repository.'));
+                process.exit(1);
+            }
+            console.log(chalk.bold('\nFound:'));
+            if (hasCommands)
+                console.log(`  ${commands.length} commands`);
+            if (hasSkills)
+                console.log(`  ${skills.length} skills`);
+            if (hasHooks)
+                console.log(`  ${hooks.shared.length + Object.values(hooks.agentSpecific).flat().length} hooks`);
+            const agents = options.agents
+                ? options.agents.split(',')
+                : ['claude', 'codex', 'gemini'];
+            // Install commands
+            if (hasCommands) {
+                console.log(chalk.bold('\nInstalling commands...'));
+                let installed = 0;
+                for (const command of commands) {
+                    for (const agentId of agents) {
+                        if (!isCliInstalled(agentId) && agentId !== 'cursor')
+                            continue;
+                        const sourcePath = resolveCommandSource(localPath, command.name, agentId);
+                        if (sourcePath) {
+                            installCommand(sourcePath, agentId, command.name, 'symlink');
+                            installed++;
+                        }
+                    }
+                }
+                console.log(`  Installed ${installed} command instances`);
+            }
+            // Install skills
+            if (hasSkills) {
+                console.log(chalk.bold('\nInstalling skills...'));
+                for (const skill of skills) {
+                    const result = installSkill(skill.path, skill.name, agents);
+                    if (result.success) {
+                        console.log(`  ${chalk.green('+')} ${skill.name}`);
+                    }
+                    else {
+                        console.log(`  ${chalk.red('x')} ${skill.name}: ${result.error}`);
+                    }
+                }
+            }
+            // Install hooks
+            if (hasHooks) {
+                console.log(chalk.bold('\nInstalling hooks...'));
+                const hookAgents = agents.filter((id) => AGENTS[id].supportsHooks);
+                const result = await installHooks(localPath, hookAgents, { scope: 'user' });
+                console.log(`  Installed ${result.installed.length} hooks`);
+            }
+            console.log(chalk.green('\nPackage installed.'));
+        }
+    }
+    catch (err) {
+        spinner.fail('Installation failed');
+        console.error(chalk.red(err.message));
+        process.exit(1);
+    }
+});
 program.parse();
 //# sourceMappingURL=index.js.map