@orchestra-research/ai-research-skills 1.0.0 → 1.0.3

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@orchestra-research/ai-research-skills",
-  "version": "1.0.0",
+  "version": "1.0.3",
   "description": "Install AI research engineering skills to your coding agents (Claude Code, Cursor, Gemini CLI, and more)",
   "main": "src/index.js",
   "bin": {

package/src/index.js

@@ -11,13 +11,16 @@ import {
   askMainMenuAction,
   askSelectAgents,
   askAfterAction,
+  askUninstallChoice,
+  askSelectSkillsToUninstall,
+  askConfirmUninstall,
   parseArgs,
   CATEGORIES,
   INDIVIDUAL_SKILLS,
   QUICK_START_SKILLS,
   getTotalSkillCount,
 } from './prompts.js';
-import { installSkills, installSpecificSkills, listInstalledSkills, getAllCategoryIds } from './installer.js';
+import { installSkills, installSpecificSkills, listInstalledSkills, getAllCategoryIds, updateInstalledSkills, uninstallAllSkills, uninstallSpecificSkills, getInstalledSkillPaths, getInstalledSkillsForSelection } from './installer.js';
 
 /**
  * Sleep utility
@@ -77,14 +80,20 @@ async function interactiveFlow() {
     }
 
     if (menuAction === 'update') {
-      // Update all skills
+      // Update only installed skills
       showMenuHeader();
-      console.log(chalk.cyan('    Updating all skills...'));
-      console.log();
-      const categories = getAllCategoryIds();
-      await installSkills(categories, agents);
-      console.log();
-      console.log(chalk.green('    ✓ All skills updated!'));
+      const installedPaths = getInstalledSkillPaths();
+      if (installedPaths.length === 0) {
+        console.log(chalk.yellow('    No skills installed to update.'));
+        console.log();
+        console.log(chalk.dim('    Install some skills first.'));
+      } else {
+        console.log(chalk.cyan(`    Updating ${installedPaths.length} installed skills...`));
+        console.log();
+        await updateInstalledSkills(agents);
+        console.log();
+        console.log(chalk.green('    ✓ All installed skills updated!'));
+      }
       const afterUpdate = await askAfterAction();
       if (afterUpdate === 'exit') {
         console.log(chalk.dim('              Goodbye!'));
@@ -94,6 +103,69 @@ async function interactiveFlow() {
       continue step2_menu;
     }
 
+    if (menuAction === 'uninstall') {
+      // Uninstall skills
+      step_uninstall:
+      while (true) {
+        showMenuHeader();
+        const installedSkills = getInstalledSkillsForSelection();
+
+        if (installedSkills.length === 0) {
+          console.log(chalk.yellow('    No skills installed to uninstall.'));
+          break;
+        }
+
+        const uninstallChoice = await askUninstallChoice();
+
+        if (uninstallChoice === 'back') {
+          break;
+        }
+
+        if (uninstallChoice === 'all') {
+          // Uninstall everything
+          const confirmAction = await askConfirmUninstall(installedSkills.length);
+          if (confirmAction === 'confirm') {
+            console.log();
+            await uninstallAllSkills(agents);
+            console.log();
+            console.log(chalk.green('    ✓ All skills uninstalled!'));
+          }
+          break;
+        }
+
+        if (uninstallChoice === 'select') {
+          // Select specific skills to uninstall
+          showMenuHeader();
+          const result = await askSelectSkillsToUninstall(installedSkills);
+
+          if (result.action === 'back') {
+            continue step_uninstall;
+          }
+          if (result.action === 'retry') {
+            continue step_uninstall;
+          }
+
+          // Confirm uninstall
+          const confirmAction = await askConfirmUninstall(result.skills.length);
+          if (confirmAction === 'confirm') {
+            console.log();
+            await uninstallSpecificSkills(result.skills, agents);
+            console.log();
+            console.log(chalk.green(`    ✓ ${result.skills.length} skill${result.skills.length !== 1 ? 's' : ''} uninstalled!`));
+          }
+          break;
+        }
+      }
+
+      const afterUninstall = await askAfterAction();
+      if (afterUninstall === 'exit') {
+        console.log(chalk.dim('              Goodbye!'));
+        console.log();
+        return;
+      }
+      continue step2_menu;
+    }
+
     // STEP 3: Choose what to install (menuAction === 'install')
     step3_choice:
     while (true) {
@@ -220,14 +292,18 @@ async function commandMode(options) {
   }
 
   if (options.command === 'update') {
-    console.log(chalk.cyan('Updating skills...'));
     const agents = detectAgents();
     if (agents.length === 0) {
       console.log(chalk.yellow('No agents detected.'));
       return;
     }
-    const categories = getAllCategoryIds();
-    await installSkills(categories, agents);
+    const installedPaths = getInstalledSkillPaths();
+    if (installedPaths.length === 0) {
+      console.log(chalk.yellow('No skills installed to update.'));
+      return;
+    }
+    console.log(chalk.cyan(`Updating ${installedPaths.length} installed skills...`));
+    await updateInstalledSkills(agents);
     console.log(chalk.green('✓ Skills updated!'));
     return;
   }

package/src/installer.js

@@ -1,11 +1,11 @@
-import { existsSync, mkdirSync, symlinkSync, readdirSync, readFileSync, writeFileSync, rmSync } from 'fs';
+import { existsSync, mkdirSync, symlinkSync, readdirSync, readFileSync, writeFileSync, rmSync, lstatSync } from 'fs';
 import { homedir } from 'os';
 import { join, basename, dirname } from 'path';
 import { execSync } from 'child_process';
 import chalk from 'chalk';
 import ora from 'ora';
 
-const REPO_URL = 'https://github.com/zechenzhangAGI/AI-research-SKILLs';
+const REPO_URL = 'https://github.com/Orchestra-Research/AI-research-SKILLs';
 const CANONICAL_DIR = join(homedir(), '.orchestra', 'skills');
 const LOCK_FILE = join(homedir(), '.orchestra', '.lock.json');
 
@@ -389,3 +389,223 @@ export function getAllCategoryIds() {
     '20-ml-paper-writing',
   ];
 }
+
+/**
+ * Get installed skill paths for updating
+ * Returns array like ['06-post-training/verl', '20-ml-paper-writing']
+ */
+export function getInstalledSkillPaths() {
+  if (!existsSync(CANONICAL_DIR)) {
+    return [];
+  }
+
+  const skillPaths = [];
+  const categories = readdirSync(CANONICAL_DIR, { withFileTypes: true })
+    .filter(d => d.isDirectory())
+    .map(d => d.name);
+
+  for (const category of categories) {
+    const categoryPath = join(CANONICAL_DIR, category);
+
+    // Check if it's a standalone skill (has SKILL.md directly)
+    const standaloneSkill = join(categoryPath, 'SKILL.md');
+    if (existsSync(standaloneSkill)) {
+      skillPaths.push(category);
+    } else {
+      // It's a category with nested skills
+      const skills = readdirSync(categoryPath, { withFileTypes: true })
+        .filter(d => d.isDirectory() && existsSync(join(categoryPath, d.name, 'SKILL.md')))
+        .map(d => d.name);
+
+      for (const skill of skills) {
+        skillPaths.push(`${category}/${skill}`);
+      }
+    }
+  }
+
+  return skillPaths;
+}
+
+/**
+ * Update only installed skills (re-download from GitHub)
+ */
+export async function updateInstalledSkills(agents) {
+  const installedPaths = getInstalledSkillPaths();
+
+  if (installedPaths.length === 0) {
+    console.log(chalk.yellow('    No skills installed to update.'));
+    return 0;
+  }
+
+  const spinner = ora('Updating from GitHub...').start();
+
+  try {
+    // Download only the installed skills
+    const skills = await downloadSpecificSkills(installedPaths, spinner);
+    spinner.succeed(`Updated ${skills.length} skills`);
+
+    // Re-create symlinks for each agent
+    spinner.start('Refreshing symlinks...');
+
+    for (const agent of agents) {
+      const count = createSymlinks(agent, skills, spinner);
+      console.log(`    ${chalk.green('✓')} ${agent.name.padEnd(14)} ${chalk.dim('→')} ${agent.skillsPath.replace(homedir(), '~').padEnd(25)} ${chalk.green(count + ' skills')}`);
+    }
+
+    spinner.stop();
+
+    // Update lock file
+    const lock = readLock();
+    lock.version = '1.0.0';
+    lock.installedAt = new Date().toISOString();
+    lock.skills = skills;
+    lock.agents = agents.map(a => a.id);
+    writeLock(lock);
+
+    return skills.length;
+  } catch (error) {
+    spinner.fail('Update failed');
+    throw error;
+  }
+}
+
+/**
+ * Uninstall all skills
+ */
+export async function uninstallAllSkills(agents) {
+  const spinner = ora('Removing skills...').start();
+
+  try {
+    // Remove symlinks from each agent
+    for (const agent of agents) {
+      if (existsSync(agent.skillsPath)) {
+        const entries = readdirSync(agent.skillsPath, { withFileTypes: true });
+        for (const entry of entries) {
+          const linkPath = join(agent.skillsPath, entry.name);
+          // Only remove if it's a symlink pointing to our canonical dir
+          try {
+            const stats = lstatSync(linkPath);
+            if (stats.isSymbolicLink()) {
+              rmSync(linkPath, { force: true });
+            }
+          } catch {
+            // Ignore errors
+          }
+        }
+      }
+      console.log(`    ${chalk.green('✓')} Removed symlinks from ${agent.name}`);
+    }
+
+    // Remove canonical skills directory
+    if (existsSync(CANONICAL_DIR)) {
+      rmSync(CANONICAL_DIR, { recursive: true, force: true });
+      console.log(`    ${chalk.green('✓')} Removed ${CANONICAL_DIR.replace(homedir(), '~')}`);
+    }
+
+    // Remove lock file
+    if (existsSync(LOCK_FILE)) {
+      rmSync(LOCK_FILE, { force: true });
+    }
+
+    spinner.stop();
+    return true;
+  } catch (error) {
+    spinner.fail('Uninstall failed');
+    throw error;
+  }
+}
+
+/**
+ * Uninstall specific skills
+ * @param {Array<string>} skillPaths - Paths like ['06-post-training/verl', '20-ml-paper-writing']
+ * @param {Array} agents - List of agents to remove symlinks from
+ */
+export async function uninstallSpecificSkills(skillPaths, agents) {
+  const spinner = ora('Removing selected skills...').start();
+
+  try {
+    for (const skillPath of skillPaths) {
+      const parts = skillPath.split('/');
+      const categoryId = parts[0];
+      const skillName = parts[1] || null;
+
+      // Determine the link name (what appears in agent's skills folder)
+      const linkName = skillName || categoryId;
+
+      // Remove symlinks from each agent
+      for (const agent of agents) {
+        const linkPath = join(agent.skillsPath, linkName);
+        try {
+          if (existsSync(linkPath)) {
+            const stats = lstatSync(linkPath);
+            if (stats.isSymbolicLink()) {
+              rmSync(linkPath, { force: true });
+            }
+          }
+        } catch {
+          // Ignore errors
+        }
+      }
+
+      // Remove from canonical directory
+      if (skillName) {
+        // Nested skill like '06-post-training/verl'
+        const skillDir = join(CANONICAL_DIR, categoryId, skillName);
+        if (existsSync(skillDir)) {
+          rmSync(skillDir, { recursive: true, force: true });
+        }
+        // Clean up empty category folder
+        const categoryDir = join(CANONICAL_DIR, categoryId);
+        if (existsSync(categoryDir)) {
+          const remaining = readdirSync(categoryDir);
+          if (remaining.length === 0) {
+            rmSync(categoryDir, { recursive: true, force: true });
+          }
+        }
+      } else {
+        // Standalone skill like '20-ml-paper-writing'
+        const skillDir = join(CANONICAL_DIR, categoryId);
+        if (existsSync(skillDir)) {
+          rmSync(skillDir, { recursive: true, force: true });
+        }
+      }
+
+      spinner.text = `Removed ${linkName}`;
+    }
+
+    spinner.succeed(`Removed ${skillPaths.length} skill${skillPaths.length !== 1 ? 's' : ''}`);
+
+    // Update lock file
+    const lock = readLock();
+    if (lock.skills) {
+      lock.skills = lock.skills.filter(s => {
+        const path = s.standalone ? s.category : `${s.category}/${s.skill}`;
+        return !skillPaths.includes(path);
+      });
+      writeLock(lock);
+    }
+
+    return skillPaths.length;
+  } catch (error) {
+    spinner.fail('Uninstall failed');
+    throw error;
+  }
+}
+
+/**
+ * Get installed skills with display info for selection
+ * Returns array of { path, name, category } for UI
+ */
+export function getInstalledSkillsForSelection() {
+  const paths = getInstalledSkillPaths();
+  return paths.map(path => {
+    const parts = path.split('/');
+    if (parts.length === 1) {
+      // Standalone skill
+      return { path, name: parts[0], category: 'Standalone', standalone: true };
+    } else {
+      // Nested skill
+      return { path, name: parts[1], category: parts[0], standalone: false };
+    }
+  });
+}

package/src/prompts.js

@@ -104,7 +104,8 @@ export async function askMainMenuAction() {
       choices: [
         { name: 'Install new skills', value: 'install' },
         { name: 'View installed skills', value: 'view' },
-        { name: 'Update all skills', value: 'update' },
+        { name: 'Update installed skills', value: 'update' },
+        { name: 'Uninstall all skills', value: 'uninstall' },
         new inquirer.Separator(' '),
         { name: chalk.dim('Exit'), value: 'exit' },
       ],
@@ -114,6 +115,98 @@ export async function askMainMenuAction() {
   return action;
 }
 
+/**
+ * Ask what to uninstall
+ */
+export async function askUninstallChoice() {
+  console.log();
+  console.log(chalk.dim('    What would you like to uninstall?'));
+  console.log();
+
+  const { choice } = await inquirer.prompt([
+    {
+      type: 'list',
+      name: 'choice',
+      message: ' ',
+      choices: [
+        { name: 'Select specific skills', value: 'select' },
+        { name: chalk.red('Uninstall everything'), value: 'all' },
+        new inquirer.Separator(' '),
+        { name: chalk.dim('← Back'), value: 'back' },
+      ],
+      prefix: '   ',
+    },
+  ]);
+  return choice;
+}
+
+/**
+ * Ask which installed skills to uninstall
+ */
+export async function askSelectSkillsToUninstall(installedSkills) {
+  console.log();
+  console.log(chalk.dim('    Select skills to uninstall:'));
+  console.log(chalk.dim('    (Space to select, Enter to confirm)'));
+  console.log();
+
+  const { skills } = await inquirer.prompt([
+    {
+      type: 'checkbox',
+      name: 'skills',
+      message: ' ',
+      choices: installedSkills.map(skill => ({
+        name: `${skill.name.padEnd(25)} ${chalk.dim(skill.category)}`,
+        value: skill.path,
+        short: skill.name,
+      })),
+      prefix: '   ',
+      pageSize: 15,
+    },
+  ]);
+
+  if (skills.length === 0) {
+    console.log();
+    const { action } = await inquirer.prompt([
+      {
+        type: 'list',
+        name: 'action',
+        message: chalk.yellow('No skills selected'),
+        choices: [
+          { name: 'Try again', value: 'retry' },
+          { name: chalk.dim('← Back'), value: 'back' },
+        ],
+        prefix: '   ',
+      },
+    ]);
+    return { skills: [], action };
+  }
+
+  return { skills, action: 'confirm' };
+}
+
+/**
+ * Ask to confirm uninstall
+ */
+export async function askConfirmUninstall(count) {
+  console.log();
+  console.log(chalk.yellow(`    This will remove ${count} skill${count !== 1 ? 's' : ''} and their symlinks.`));
+  console.log();
+
+  const { action } = await inquirer.prompt([
+    {
+      type: 'list',
+      name: 'action',
+      message: ' ',
+      choices: [
+        { name: chalk.red('Yes, uninstall'), value: 'confirm' },
+        { name: chalk.dim('← Back'), value: 'back' },
+      ],
+      prefix: '   ',
+    },
+  ]);
+  return action;
+}
+
 /**
  * Ask what to install
  */