Merge f0ad64efc4 into 2d134314c9

Prevents invalid YAML when agentName or skillName contains quotes or
other special characters. Aligns the fallback path in transformToSkillFormat
and installCustomAgentLauncher with the existing yaml.stringify usage on
the main code path.

.gitignore

@@ -36,6 +36,7 @@ cursor
 CLAUDE.local.md
 .serena/
 .claude/settings.local.json
+.agents
 
 z*/
 

package.json

@@ -25,6 +25,7 @@
   },
   "scripts": {
     "bmad:install": "node tools/cli/bmad-cli.js install",
+    "bmad:uninstall": "node tools/cli/bmad-cli.js uninstall",
     "docs:build": "node tools/build-docs.mjs",
     "docs:dev": "astro dev --root website",
     "docs:fix-links": "node tools/fix-doc-links.js",

test/test-codex-transform.js

@@ -0,0 +1,145 @@
+/**
+ * Tests for CodexSetup.transformToSkillFormat
+ *
+ * Validates that descriptions round-trip correctly through parse/stringify,
+ * producing valid YAML regardless of input quoting style.
+ *
+ * Usage: node test/test-codex-transform.js
+ */
+
+const path = require('node:path');
+const yaml = require('yaml');
+
+// ANSI colors
+const colors = {
+  reset: '\u001B[0m',
+  green: '\u001B[32m',
+  red: '\u001B[31m',
+  cyan: '\u001B[36m',
+  dim: '\u001B[2m',
+};
+
+let passed = 0;
+let failed = 0;
+
+function assert(condition, testName, detail) {
+  if (condition) {
+    console.log(`  ${colors.green}PASS${colors.reset} ${testName}`);
+    passed++;
+  } else {
+    console.log(`  ${colors.red}FAIL${colors.reset} ${testName}`);
+    if (detail) console.log(`       ${colors.dim}${detail}${colors.reset}`);
+    failed++;
+  }
+}
+
+/**
+ * Parse the output frontmatter and return the description value.
+ * Validates the output is well-formed YAML that parses back correctly.
+ */
+function parseOutputDescription(output) {
+  const match = output.match(/^---\r?\n([\s\S]*?)\r?\n---/);
+  if (!match) return null;
+  const parsed = yaml.parse(match[1]);
+  return parsed?.description;
+}
+
+// Import the class under test
+const { CodexSetup } = require(path.join(__dirname, '..', 'tools', 'cli', 'installers', 'lib', 'ide', 'codex.js'));
+
+const setup = new CodexSetup();
+
+console.log(`\n${colors.cyan}CodexSetup.transformToSkillFormat tests${colors.reset}\n`);
+
+// --- Simple description, no quotes ---
+{
+  const input = `---\ndescription: A simple description\n---\n\nBody content here.`;
+  const result = setup.transformToSkillFormat(input, 'my-skill');
+  const desc = parseOutputDescription(result);
+  assert(desc === 'A simple description', 'simple description round-trips', `got description: ${JSON.stringify(desc)}`);
+  assert(result.includes('\nBody content here.'), 'body preserved for simple description');
+}
+
+// --- Description with embedded single quotes (from double-quoted YAML input) ---
+{
+  const input = `---\ndescription: "can't stop won't stop"\n---\n\nBody content here.`;
+  const result = setup.transformToSkillFormat(input, 'my-skill');
+  const desc = parseOutputDescription(result);
+  assert(desc === "can't stop won't stop", 'description with apostrophes round-trips', `got description: ${JSON.stringify(desc)}`);
+  assert(result.includes('\nBody content here.'), 'body preserved for quoted description');
+}
+
+// --- Description with embedded single quote ---
+{
+  const input = `---\ndescription: "it's a test"\n---\n\nBody.`;
+  const result = setup.transformToSkillFormat(input, 'test-skill');
+  const desc = parseOutputDescription(result);
+  assert(desc === "it's a test", 'description with apostrophe round-trips', `got description: ${JSON.stringify(desc)}`);
+}
+
+// --- Single-quoted input with pre-escaped apostrophe (YAML '' escape) ---
+{
+  const input = `---\ndescription: 'don''t panic'\n---\n\nBody.`;
+  const result = setup.transformToSkillFormat(input, 'test-skill');
+  const desc = parseOutputDescription(result);
+  assert(desc === "don't panic", 'single-quoted escaped apostrophe round-trips', `got description: ${JSON.stringify(desc)}`);
+}
+
+// --- Verify name is set correctly ---
+{
+  const input = `---\ndescription: test\n---\n\nBody.`;
+  const result = setup.transformToSkillFormat(input, 'my-custom-skill');
+  const match = result.match(/^---\n([\s\S]*?)\n---/);
+  const parsed = yaml.parse(match[1]);
+  assert(parsed.name === 'my-custom-skill', 'name field matches skillName argument', `got name: ${JSON.stringify(parsed.name)}`);
+}
+
+// --- Extra frontmatter keys are stripped ---
+{
+  const input = `---\ndescription: foo\ndisable-model-invocation: true\ncustom-field: bar\n---\n\nBody.`;
+  const result = setup.transformToSkillFormat(input, 'strip-extra');
+  const desc = parseOutputDescription(result);
+  assert(desc === 'foo', 'description preserved when extra keys present', `got description: ${JSON.stringify(desc)}`);
+  const match = result.match(/^---\n([\s\S]*?)\n---/);
+  const parsed = yaml.parse(match[1]);
+  assert(parsed.name === 'strip-extra', 'name equals skillName after stripping extras', `got name: ${JSON.stringify(parsed.name)}`);
+  assert(!('disable-model-invocation' in parsed), 'disable-model-invocation stripped', `keys: ${Object.keys(parsed).join(', ')}`);
+  assert(!('custom-field' in parsed), 'custom-field stripped', `keys: ${Object.keys(parsed).join(', ')}`);
+  const keys = Object.keys(parsed).sort();
+  assert(
+    keys.length === 2 && keys[0] === 'description' && keys[1] === 'name',
+    'only name and description remain',
+    `keys: ${keys.join(', ')}`,
+  );
+}
+
+// --- No frontmatter wraps content ---
+{
+  const input = 'Just some content without frontmatter.';
+  const result = setup.transformToSkillFormat(input, 'bare-skill');
+  const desc = parseOutputDescription(result);
+  assert(desc === 'bare-skill', 'no-frontmatter fallback uses skillName as description', `got description: ${JSON.stringify(desc)}`);
+  assert(result.includes('Just some content without frontmatter.'), 'body preserved when no frontmatter');
+}
+
+// --- No frontmatter with single-quote in skillName ---
+{
+  const input = 'Body content for the skill.';
+  const result = setup.transformToSkillFormat(input, "it's-a-task");
+  const desc = parseOutputDescription(result);
+  assert(desc === "it's-a-task", 'no-frontmatter skillName with single quote round-trips', `got description: ${JSON.stringify(desc)}`);
+  assert(result.includes('Body content for the skill.'), 'body preserved for single-quote skillName');
+}
+
+// --- CRLF frontmatter is parsed correctly (Windows line endings) ---
+{
+  const input = '---\r\ndescription: windows line endings\r\n---\r\n\r\nBody.';
+  const result = setup.transformToSkillFormat(input, 'crlf-skill');
+  const desc = parseOutputDescription(result);
+  assert(desc === 'windows line endings', 'CRLF frontmatter parses correctly', `got description: ${JSON.stringify(desc)}`);
+  assert(result.includes('Body.'), 'body preserved for CRLF input');
+}
+
+// --- Summary ---
+console.log(`\n${passed} passed, ${failed} failed\n`);
+process.exit(failed > 0 ? 1 : 0);

test/test-codex-write-skills.js

@@ -0,0 +1,216 @@
+/**
+ * Tests for CodexSetup.writeSkillArtifacts
+ *
+ * Validates directory creation, SKILL.md file writing, type filtering,
+ * and integration with transformToSkillFormat.
+ *
+ * Usage: node test/test-codex-write-skills.js
+ */
+
+const path = require('node:path');
+const fs = require('fs-extra');
+const os = require('node:os');
+const yaml = require('yaml');
+
+// ANSI colors
+const colors = {
+  reset: '\u001B[0m',
+  green: '\u001B[32m',
+  red: '\u001B[31m',
+  cyan: '\u001B[36m',
+  dim: '\u001B[2m',
+};
+
+let passed = 0;
+let failed = 0;
+
+function assert(condition, testName, detail) {
+  if (condition) {
+    console.log(`  ${colors.green}PASS${colors.reset} ${testName}`);
+    passed++;
+  } else {
+    console.log(`  ${colors.red}FAIL${colors.reset} ${testName}`);
+    if (detail) console.log(`       ${colors.dim}${detail}${colors.reset}`);
+    failed++;
+  }
+}
+
+// Import the class under test
+const { CodexSetup } = require(path.join(__dirname, '..', 'tools', 'cli', 'installers', 'lib', 'ide', 'codex.js'));
+
+const setup = new CodexSetup();
+
+// Create a temp directory for each test run
+let tmpDir;
+
+async function createTmpDir() {
+  tmpDir = path.join(os.tmpdir(), `bmad-test-skills-${Date.now()}`);
+  await fs.ensureDir(tmpDir);
+  return tmpDir;
+}
+
+async function cleanTmpDir() {
+  if (tmpDir) {
+    await fs.remove(tmpDir);
+  }
+}
+
+async function runTests() {
+  console.log(`\n${colors.cyan}CodexSetup.writeSkillArtifacts tests${colors.reset}\n`);
+
+  // --- Writes a single artifact as a skill directory with SKILL.md ---
+  {
+    const destDir = await createTmpDir();
+    const artifacts = [
+      {
+        type: 'task',
+        relativePath: 'bmm/tasks/create-story.md',
+        content: '---\ndescription: Create a user story\n---\n\nStory creation instructions.',
+      },
+    ];
+    const count = await setup.writeSkillArtifacts(destDir, artifacts, 'task');
+    assert(count === 1, 'single artifact returns count 1');
+
+    const skillDir = path.join(destDir, 'bmad-bmm-create-story');
+    assert(await fs.pathExists(skillDir), 'skill directory created');
+
+    const skillFile = path.join(skillDir, 'SKILL.md');
+    assert(await fs.pathExists(skillFile), 'SKILL.md file created');
+
+    const content = await fs.readFile(skillFile, 'utf8');
+    const fmMatch = content.match(/^---\n([\s\S]*?)\n---/);
+    assert(fmMatch !== null, 'SKILL.md has frontmatter');
+
+    const parsed = yaml.parse(fmMatch[1]);
+    assert(parsed.name === 'bmad-bmm-create-story', 'name matches skill directory name', `got: ${parsed.name}`);
+    assert(parsed.description === 'Create a user story', 'description preserved', `got: ${parsed.description}`);
+    assert(content.includes('Story creation instructions.'), 'body content preserved');
+    await cleanTmpDir();
+  }
+
+  // --- Filters artifacts by type ---
+  {
+    const destDir = await createTmpDir();
+    const artifacts = [
+      {
+        type: 'task',
+        relativePath: 'bmm/tasks/create-story.md',
+        content: '---\ndescription: A task\n---\n\nTask body.',
+      },
+      {
+        type: 'workflow-command',
+        relativePath: 'bmm/workflows/plan-project.md',
+        content: '---\ndescription: A workflow\n---\n\nWorkflow body.',
+      },
+      {
+        type: 'agent-launcher',
+        relativePath: 'bmm/agents/pm.md',
+        content: '---\ndescription: An agent\n---\n\nAgent body.',
+      },
+    ];
+    const count = await setup.writeSkillArtifacts(destDir, artifacts, 'task');
+    assert(count === 1, 'only matching type is written when filtering for task');
+
+    const entries = await fs.readdir(destDir);
+    assert(entries.length === 1, 'only one skill directory created', `got ${entries.length}: ${entries.join(', ')}`);
+    assert(entries[0] === 'bmad-bmm-create-story', 'correct artifact was written', `got: ${entries[0]}`);
+    await cleanTmpDir();
+  }
+
+  // --- Writes multiple artifacts of the same type ---
+  {
+    const destDir = await createTmpDir();
+    const artifacts = [
+      {
+        type: 'workflow-command',
+        relativePath: 'bmm/workflows/plan-project.md',
+        content: '---\ndescription: Plan\n---\n\nPlan body.',
+      },
+      {
+        type: 'workflow-command',
+        relativePath: 'core/workflows/review.md',
+        content: '---\ndescription: Review\n---\n\nReview body.',
+      },
+    ];
+    const count = await setup.writeSkillArtifacts(destDir, artifacts, 'workflow-command');
+    assert(count === 2, 'two artifacts written');
+
+    const entries = new Set((await fs.readdir(destDir)).sort());
+    assert(entries.has('bmad-bmm-plan-project'), 'first skill directory exists');
+    assert(entries.has('bmad-review'), 'second skill directory exists (core module)');
+    await cleanTmpDir();
+  }
+
+  // --- Returns 0 when no artifacts match type ---
+  {
+    const destDir = await createTmpDir();
+    const artifacts = [
+      {
+        type: 'agent-launcher',
+        relativePath: 'bmm/agents/pm.md',
+        content: '---\ndescription: An agent\n---\n\nBody.',
+      },
+    ];
+    const count = await setup.writeSkillArtifacts(destDir, artifacts, 'task');
+    assert(count === 0, 'returns 0 when no types match');
+
+    const entries = await fs.readdir(destDir);
+    assert(entries.length === 0, 'no directories created when no types match');
+    await cleanTmpDir();
+  }
+
+  // --- Handles empty artifacts array ---
+  {
+    const destDir = await createTmpDir();
+    const count = await setup.writeSkillArtifacts(destDir, [], 'task');
+    assert(count === 0, 'returns 0 for empty artifacts array');
+    await cleanTmpDir();
+  }
+
+  // --- Artifacts without type field are always written ---
+  {
+    const destDir = await createTmpDir();
+    const artifacts = [
+      {
+        relativePath: 'bmm/tasks/no-type.md',
+        content: '---\ndescription: No type field\n---\n\nBody.',
+      },
+    ];
+    const count = await setup.writeSkillArtifacts(destDir, artifacts, 'task');
+    assert(count === 1, 'artifact without type field is written (no filtering)');
+    await cleanTmpDir();
+  }
+
+  // --- Content without frontmatter gets minimal frontmatter added ---
+  {
+    const destDir = await createTmpDir();
+    const artifacts = [
+      {
+        type: 'task',
+        relativePath: 'bmm/tasks/bare.md',
+        content: 'Just plain content, no frontmatter.',
+      },
+    ];
+    const count = await setup.writeSkillArtifacts(destDir, artifacts, 'task');
+    assert(count === 1, 'bare content artifact written');
+
+    const skillFile = path.join(destDir, 'bmad-bmm-bare', 'SKILL.md');
+    const content = await fs.readFile(skillFile, 'utf8');
+    const fmMatch = content.match(/^---\n([\s\S]*?)\n---/);
+    assert(fmMatch !== null, 'frontmatter added to bare content');
+
+    const parsed = yaml.parse(fmMatch[1]);
+    assert(parsed.name === 'bmad-bmm-bare', 'name set for bare content', `got: ${parsed.name}`);
+    assert(content.includes('Just plain content, no frontmatter.'), 'original content preserved');
+    await cleanTmpDir();
+  }
+
+  // --- Summary ---
+  console.log(`\n${passed} passed, ${failed} failed\n`);
+  process.exit(failed > 0 ? 1 : 0);
+}
+
+runTests().catch((error) => {
+  console.error('Test runner error:', error);
+  process.exit(1);
+});

tools/cli/commands/uninstall.js

@@ -0,0 +1,167 @@
+const path = require('node:path');
+const fs = require('fs-extra');
+const prompts = require('../lib/prompts');
+const { Installer } = require('../installers/lib/core/installer');
+
+const installer = new Installer();
+
+module.exports = {
+  command: 'uninstall',
+  description: 'Remove BMAD installation from the current project',
+  options: [
+    ['-y, --yes', 'Remove all BMAD components without prompting (preserves user artifacts)'],
+    ['--directory <path>', 'Project directory (default: current directory)'],
+  ],
+  action: async (options) => {
+    try {
+      let projectDir;
+
+      if (options.directory) {
+        // Explicit --directory flag takes precedence
+        projectDir = path.resolve(options.directory);
+      } else if (options.yes) {
+        // Non-interactive mode: use current directory
+        projectDir = process.cwd();
+      } else {
+        // Interactive: ask user which directory to uninstall from
+        // select() handles cancellation internally (exits process)
+        const dirChoice = await prompts.select({
+          message: 'Where do you want to uninstall BMAD from?',
+          choices: [
+            { value: 'cwd', name: `Current directory (${process.cwd()})` },
+            { value: 'other', name: 'Another directory...' },
+          ],
+        });
+
+        if (dirChoice === 'other') {
+          // text() handles cancellation internally (exits process)
+          const customDir = await prompts.text({
+            message: 'Enter the project directory path:',
+            placeholder: process.cwd(),
+            validate: (value) => {
+              if (!value || value.trim().length === 0) return 'Directory path is required';
+            },
+          });
+
+          projectDir = path.resolve(customDir.trim());
+        } else {
+          projectDir = process.cwd();
+        }
+      }
+
+      if (!(await fs.pathExists(projectDir))) {
+        await prompts.log.error(`Directory does not exist: ${projectDir}`);
+        process.exit(1);
+      }
+
+      const { bmadDir } = await installer.findBmadDir(projectDir);
+
+      if (!(await fs.pathExists(bmadDir))) {
+        await prompts.log.warn('No BMAD installation found.');
+        process.exit(0);
+      }
+
+      const existingInstall = await installer.getStatus(projectDir);
+      const version = existingInstall.version || 'unknown';
+      const modules = (existingInstall.modules || []).map((m) => m.id || m.name).join(', ');
+      const ides = (existingInstall.ides || []).join(', ');
+
+      const outputFolder = await installer.getOutputFolder(projectDir);
+
+      await prompts.intro('BMAD Uninstall');
+      await prompts.note(`Version: ${version}\nModules: ${modules}\nIDE integrations: ${ides}`, 'Current Installation');
+
+      let removeModules = true;
+      let removeIdeConfigs = true;
+      let removeOutputFolder = false;
+
+      if (!options.yes) {
+        // multiselect() handles cancellation internally (exits process)
+        const selected = await prompts.multiselect({
+          message: 'Select components to remove:',
+          options: [
+            {
+              value: 'modules',
+              label: `BMAD Modules & data (${installer.bmadFolderName}/)`,
+              hint: 'Core installation, agents, workflows, config',
+            },
+            { value: 'ide', label: 'IDE integrations', hint: ides || 'No IDEs configured' },
+            { value: 'output', label: `User artifacts (${outputFolder}/)`, hint: 'WARNING: Contains your work products' },
+          ],
+          initialValues: ['modules', 'ide'],
+          required: true,
+        });
+
+        removeModules = selected.includes('modules');
+        removeIdeConfigs = selected.includes('ide');
+        removeOutputFolder = selected.includes('output');
+
+        const red = (s) => `\u001B[31m${s}\u001B[0m`;
+        await prompts.note(
+          red('💀 This action is IRREVERSIBLE! Removed files cannot be recovered!') +
+            '\n' +
+            red('💀 IDE configurations and modules will need to be reinstalled.') +
+            '\n' +
+            red('💀 User artifacts are preserved unless explicitly selected.'),
+          '!! DESTRUCTIVE ACTION !!',
+        );
+
+        const confirmed = await prompts.confirm({
+          message: 'Proceed with uninstall?',
+          default: false,
+        });
+
+        if (!confirmed) {
+          await prompts.outro('Uninstall cancelled.');
+          process.exit(0);
+        }
+      }
+
+      // Phase 1: IDE integrations
+      if (removeIdeConfigs) {
+        const s = await prompts.spinner();
+        s.start('Removing IDE integrations...');
+        await installer.uninstallIdeConfigs(projectDir, existingInstall, { silent: true });
+        s.stop(`Removed IDE integrations (${ides || 'none'})`);
+      }
+
+      // Phase 2: User artifacts
+      if (removeOutputFolder) {
+        const s = await prompts.spinner();
+        s.start(`Removing user artifacts (${outputFolder}/)...`);
+        await installer.uninstallOutputFolder(projectDir, outputFolder);
+        s.stop('User artifacts removed');
+      }
+
+      // Phase 3: BMAD modules & data (last — other phases may need _bmad/)
+      if (removeModules) {
+        const s = await prompts.spinner();
+        s.start(`Removing BMAD modules & data (${installer.bmadFolderName}/)...`);
+        await installer.uninstallModules(projectDir);
+        s.stop('Modules & data removed');
+      }
+
+      const summary = [];
+      if (removeIdeConfigs) summary.push('IDE integrations cleaned');
+      if (removeModules) summary.push('Modules & data removed');
+      if (removeOutputFolder) summary.push('User artifacts removed');
+      if (!removeOutputFolder) summary.push(`User artifacts preserved in ${outputFolder}/`);
+
+      await prompts.note(summary.join('\n'), 'Summary');
+      await prompts.outro('To reinstall, run: npx bmad-method install');
+
+      process.exit(0);
+    } catch (error) {
+      try {
+        const errorMessage = error instanceof Error ? error.message : String(error);
+        await prompts.log.error(`Uninstall failed: ${errorMessage}`);
+        if (error instanceof Error && error.stack) {
+          await prompts.log.message(error.stack);
+        }
+      } catch {
+        console.error(error instanceof Error ? error.message : error);
+      }
+      process.exit(1);
+    }
+  },
+};

tools/cli/installers/install-messages.yaml

@@ -34,7 +34,7 @@ startMessage: |
     - Subscribe on YouTube: https://www.youtube.com/@BMadCode
     - Every star & sub helps us reach more developers!
 
-  Latest updates: https://github.com/bmad-code-org/BMAD-METHOD/CHANGELOG.md
+  Latest updates: https://github.com/bmad-code-org/BMAD-METHOD/blob/main/CHANGELOG.md
 
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 

tools/cli/installers/lib/core/installer.js

@@ -1528,20 +1528,157 @@ class Installer {
   }
 
   /**
-   * Uninstall BMAD
+   * Uninstall BMAD with selective removal options
+   * @param {string} directory - Project directory
+   * @param {Object} options - Uninstall options
+   * @param {boolean} [options.removeModules=true] - Remove _bmad/ directory
+   * @param {boolean} [options.removeIdeConfigs=true] - Remove IDE configurations
+   * @param {boolean} [options.removeOutputFolder=false] - Remove user artifacts output folder
+   * @returns {Object} Result with success status and removed components
    */
-  async uninstall(directory) {
+  async uninstall(directory, options = {}) {
     const projectDir = path.resolve(directory);
     const { bmadDir } = await this.findBmadDir(projectDir);
 
-    if (await fs.pathExists(bmadDir)) {
-      await fs.remove(bmadDir);
+    if (!(await fs.pathExists(bmadDir))) {
+      return { success: false, reason: 'not-installed' };
     }
 
-    // Clean up IDE configurations
-    await this.ideManager.cleanup(projectDir);
+    // 1. DETECT: Read state BEFORE deleting anything
+    const existingInstall = await this.detector.detect(bmadDir);
+    const outputFolder = await this._readOutputFolder(bmadDir);
 
-    return { success: true };
+    const removed = { modules: false, ideConfigs: false, outputFolder: false };
+
+    // 2. IDE CLEANUP (before _bmad/ deletion so configs are accessible)
+    if (options.removeIdeConfigs !== false) {
+      await this.uninstallIdeConfigs(projectDir, existingInstall, { silent: options.silent });
+      removed.ideConfigs = true;
+    }
+
+    // 3. OUTPUT FOLDER (only if explicitly requested)
+    if (options.removeOutputFolder === true && outputFolder) {
+      removed.outputFolder = await this.uninstallOutputFolder(projectDir, outputFolder);
+    }
+
+    // 4. BMAD DIRECTORY (last, after everything that needs it)
+    if (options.removeModules !== false) {
+      removed.modules = await this.uninstallModules(projectDir);
+    }
+
+    return { success: true, removed, version: existingInstall.version };
+  }
+
+  /**
+   * Uninstall IDE configurations only
+   * @param {string} projectDir - Project directory
+   * @param {Object} existingInstall - Detection result from detector.detect()
+   * @param {Object} [options] - Options (e.g. { silent: true })
+   * @returns {Promise<Object>} Results from IDE cleanup
+   */
+  async uninstallIdeConfigs(projectDir, existingInstall, options = {}) {
+    await this.ideManager.ensureInitialized();
+    const cleanupOptions = { isUninstall: true, silent: options.silent };
+    const ideList = existingInstall.ides || [];
+    if (ideList.length > 0) {
+      return this.ideManager.cleanupByList(projectDir, ideList, cleanupOptions);
+    }
+    return this.ideManager.cleanup(projectDir, cleanupOptions);
+  }
+
+  /**
+   * Remove user artifacts output folder
+   * @param {string} projectDir - Project directory
+   * @param {string} outputFolder - Output folder name (relative)
+   * @returns {Promise<boolean>} Whether the folder was removed
+   */
+  async uninstallOutputFolder(projectDir, outputFolder) {
+    if (!outputFolder) return false;
+    const resolvedProject = path.resolve(projectDir);
+    const outputPath = path.resolve(resolvedProject, outputFolder);
+    if (!outputPath.startsWith(resolvedProject + path.sep)) {
+      return false;
+    }
+    if (await fs.pathExists(outputPath)) {
+      await fs.remove(outputPath);
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Remove the _bmad/ directory
+   * @param {string} projectDir - Project directory
+   * @returns {Promise<boolean>} Whether the directory was removed
+   */
+  async uninstallModules(projectDir) {
+    const { bmadDir } = await this.findBmadDir(projectDir);
+    if (await fs.pathExists(bmadDir)) {
+      await fs.remove(bmadDir);
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Get the configured output folder name for a project
+   * Resolves bmadDir internally from projectDir
+   * @param {string} projectDir - Project directory
+   * @returns {string} Output folder name (relative, default: '_bmad-output')
+   */
+  async getOutputFolder(projectDir) {
+    const { bmadDir } = await this.findBmadDir(projectDir);
+    return this._readOutputFolder(bmadDir);
+  }
+
+  /**
+   * Read the output_folder setting from module config files
+   * Checks bmm/config.yaml first, then other module configs
+   * @param {string} bmadDir - BMAD installation directory
+   * @returns {string} Output folder path or default
+   */
+  async _readOutputFolder(bmadDir) {
+    const yaml = require('yaml');
+
+    // Check bmm/config.yaml first (most common)
+    const bmmConfigPath = path.join(bmadDir, 'bmm', 'config.yaml');
+    if (await fs.pathExists(bmmConfigPath)) {
+      try {
+        const content = await fs.readFile(bmmConfigPath, 'utf8');
+        const config = yaml.parse(content);
+        if (config && config.output_folder) {
+          // Strip {project-root}/ prefix if present
+          return config.output_folder.replace(/^\{project-root\}[/\\]/, '');
+        }
+      } catch {
+        // Fall through to other modules
+      }
+    }
+
+    // Scan other module config.yaml files
+    try {
+      const entries = await fs.readdir(bmadDir, { withFileTypes: true });
+      for (const entry of entries) {
+        if (!entry.isDirectory() || entry.name === 'bmm' || entry.name.startsWith('_')) continue;
+        const configPath = path.join(bmadDir, entry.name, 'config.yaml');
+        if (await fs.pathExists(configPath)) {
+          try {
+            const content = await fs.readFile(configPath, 'utf8');
+            const config = yaml.parse(content);
+            if (config && config.output_folder) {
+              return config.output_folder.replace(/^\{project-root\}[/\\]/, '');
+            }
+          } catch {
+            // Continue scanning
+          }
+        }
+      }
+    } catch {
+      // Directory scan failed
+    }
+
+    // Default fallback
+    return '_bmad-output';
   }
 
   /**

tools/cli/installers/lib/ide/_config-driven.js

@@ -456,8 +456,18 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
   async cleanup(projectDir, options = {}) {
     // Clean all target directories
     if (this.installerConfig?.targets) {
+      const parentDirs = new Set();
       for (const target of this.installerConfig.targets) {
         await this.cleanupTarget(projectDir, target.target_dir, options);
+        // Track parent directories for empty-dir cleanup
+        const parentDir = path.dirname(target.target_dir);
+        if (parentDir && parentDir !== '.') {
+          parentDirs.add(parentDir);
+        }
+      }
+      // After all targets cleaned, remove empty parent directories (recursive up to projectDir)
+      for (const parentDir of parentDirs) {
+        await this.removeEmptyParents(projectDir, parentDir);
       }
     } else if (this.installerConfig?.target_dir) {
       await this.cleanupTarget(projectDir, this.installerConfig.target_dir, options);
@@ -509,6 +519,41 @@ LOAD and execute from: {project-root}/{{bmadFolderName}}/{{path}}
     if (removedCount > 0 && !options.silent) {
       await prompts.log.message(`  Cleaned ${removedCount} BMAD files from ${targetDir}`);
     }
+
+    // Remove empty directory after cleanup
+    if (removedCount > 0) {
+      try {
+        const remaining = await fs.readdir(targetPath);
+        if (remaining.length === 0) {
+          await fs.remove(targetPath);
+        }
+      } catch {
+        // Directory may already be gone or in use — skip
+      }
+    }
+  }
+  /**
+   * Recursively remove empty directories walking up from dir toward projectDir
+   * Stops at projectDir boundary — never removes projectDir itself
+   * @param {string} projectDir - Project root (boundary)
+   * @param {string} relativeDir - Relative directory to start from
+   */
+  async removeEmptyParents(projectDir, relativeDir) {
+    let current = relativeDir;
+    let last = null;
+    while (current && current !== '.' && current !== last) {
+      last = current;
+      const fullPath = path.join(projectDir, current);
+      try {
+        if (!(await fs.pathExists(fullPath))) break;
+        const remaining = await fs.readdir(fullPath);
+        if (remaining.length > 0) break;
+        await fs.rmdir(fullPath);
+      } catch {
+        break;
+      }
+      current = path.dirname(current);
+    }
   }
 }
 

tools/cli/installers/lib/ide/codex.js

@@ -7,10 +7,13 @@ const { AgentCommandGenerator } = require('./shared/agent-command-generator');
 const { TaskToolCommandGenerator } = require('./shared/task-tool-command-generator');
 const { getTasksFromBmad } = require('./shared/bmad-artifacts');
 const { toDashPath, customAgentDashName } = require('./shared/path-utils');
+const yaml = require('yaml');
 const prompts = require('../../../lib/prompts');
 
 /**
  * Codex setup handler (CLI mode)
+ * Writes BMAD artifacts as Agent Skills (agentskills.io format)
+ * into .agents/skills/ directories.
  */
 class CodexSetup extends BaseIdeSetup {
   constructor() {
@@ -23,35 +26,35 @@ class CodexSetup extends BaseIdeSetup {
    * @returns {Object} Collected configuration
    */
   async collectConfiguration(options = {}) {
-    // Non-interactive mode: use default (global)
+    // Non-interactive mode: use default (project)
     if (options.skipPrompts) {
-      return { installLocation: 'global' };
+      return { installLocation: 'project' };
     }
 
     let confirmed = false;
-    let installLocation = 'global';
+    let installLocation = 'project';
 
     while (!confirmed) {
       installLocation = await prompts.select({
-        message: 'Where would you like to install Codex CLI prompts?',
+        message: 'Where would you like to install Codex CLI skills?',
         choices: [
           {
-            name: 'Global - Simple for single project ' + '(~/.codex/prompts, but references THIS project only)',
-            value: 'global',
-          },
-          {
-            name: `Project-specific - Recommended for real work (requires CODEX_HOME=<project-dir>${path.sep}.codex)`,
+            name: 'Project-specific - Recommended (<project>/.agents/skills)',
             value: 'project',
           },
+          {
+            name: 'Global - ($HOME/.agents/skills)',
+            value: 'global',
+          },
         ],
-        default: 'global',
+        default: 'project',
       });
 
       // Show brief confirmation hint (detailed instructions available via verbose)
       if (installLocation === 'project') {
-        await prompts.log.info('Prompts installed to: <project>/.codex/prompts (requires CODEX_HOME)');
+        await prompts.log.info('Skills installed to: <project>/.agents/skills');
       } else {
-        await prompts.log.info('Prompts installed to: ~/.codex/prompts');
+        await prompts.log.info('Skills installed to: $HOME/.agents/skills');
       }
 
       // Confirm the choice
@@ -80,20 +83,21 @@ class CodexSetup extends BaseIdeSetup {
     // Always use CLI mode
     const mode = 'cli';
 
-    // Get installation location from pre-collected config or default to global
-    const installLocation = options.preCollectedConfig?.installLocation || 'global';
+    // Get installation location from pre-collected config or default to project
+    const installLocation = options.preCollectedConfig?.installLocation || 'project';
 
     const { artifacts, counts } = await this.collectClaudeArtifacts(projectDir, bmadDir, options);
 
-    const destDir = this.getCodexPromptDir(projectDir, installLocation);
+    const destDir = this.getCodexSkillsDir(projectDir, installLocation);
     await fs.ensureDir(destDir);
-    await this.clearOldBmadFiles(destDir, options);
+    await this.clearOldBmadSkills(destDir, options);
 
-    // Collect artifacts and write using underscore format
+    // Collect and write agent skills
     const agentGen = new AgentCommandGenerator(this.bmadFolderName);
     const { artifacts: agentArtifacts } = await agentGen.collectAgentArtifacts(bmadDir, options.selectedModules || []);
-    const agentCount = await agentGen.writeDashArtifacts(destDir, agentArtifacts);
+    const agentCount = await this.writeSkillArtifacts(destDir, agentArtifacts, 'agent-launcher');
 
+    // Collect and write task skills
     const tasks = await getTasksFromBmad(bmadDir, options.selectedModules || []);
     const taskArtifacts = [];
     for (const task of tasks) {
@@ -117,19 +121,23 @@ class CodexSetup extends BaseIdeSetup {
       });
     }
 
+    const ttGen = new TaskToolCommandGenerator(this.bmadFolderName);
+    const taskSkillArtifacts = taskArtifacts.map((artifact) => ({
+      ...artifact,
+      content: ttGen.generateCommandContent(artifact, artifact.type),
+    }));
+    const tasksWritten = await this.writeSkillArtifacts(destDir, taskSkillArtifacts, 'task');
+
+    // Collect and write workflow skills
     const workflowGenerator = new WorkflowCommandGenerator(this.bmadFolderName);
     const { artifacts: workflowArtifacts } = await workflowGenerator.collectWorkflowArtifacts(bmadDir);
-    const workflowCount = await workflowGenerator.writeDashArtifacts(destDir, workflowArtifacts);
-
-    // Also write tasks using underscore format
-    const ttGen = new TaskToolCommandGenerator(this.bmadFolderName);
-    const tasksWritten = await ttGen.writeDashArtifacts(destDir, taskArtifacts);
+    const workflowCount = await this.writeSkillArtifacts(destDir, workflowArtifacts, 'workflow-command');
 
     const written = agentCount + workflowCount + tasksWritten;
 
     if (!options.silent) {
       await prompts.log.success(
-        `${this.name} configured: ${counts.agents} agents, ${counts.workflows} workflows, ${counts.tasks} tasks, ${written} files → ${destDir}`,
+        `${this.name} configured: ${counts.agents} agents, ${counts.workflows} workflows, ${counts.tasks} tasks, ${written} skills → ${destDir}`,
       );
     }
 
@@ -145,13 +153,82 @@ class CodexSetup extends BaseIdeSetup {
   }
 
   /**
-   * Detect Codex installation by checking for BMAD prompt exports
+   * Write artifacts as Agent Skills (agentskills.io format).
+   * Each artifact becomes a directory containing SKILL.md.
+   * @param {string} destDir - Base skills directory
+   * @param {Array} artifacts - Artifacts to write
+   * @param {string} artifactType - Type filter (e.g., 'agent-launcher', 'workflow-command', 'task')
+   * @returns {number} Number of skills written
+   */
+  async writeSkillArtifacts(destDir, artifacts, artifactType) {
+    let writtenCount = 0;
+
+    for (const artifact of artifacts) {
+      // Filter by type if the artifact has a type field
+      if (artifact.type && artifact.type !== artifactType) {
+        continue;
+      }
+
+      // Get the dash-format name (e.g., bmad-bmm-create-prd.md) and remove .md
+      const flatName = toDashPath(artifact.relativePath);
+      const skillName = flatName.replace(/\.md$/, '');
+
+      // Create skill directory
+      const skillDir = path.join(destDir, skillName);
+      await fs.ensureDir(skillDir);
+
+      // Transform content: rewrite frontmatter for skills format
+      const skillContent = this.transformToSkillFormat(artifact.content, skillName);
+
+      // Write SKILL.md
+      await fs.writeFile(path.join(skillDir, 'SKILL.md'), skillContent);
+      writtenCount++;
+    }
+
+    return writtenCount;
+  }
+
+  /**
+   * Transform artifact content from Codex prompt format to Agent Skills format.
+   * Removes disable-model-invocation, ensures name matches directory.
+   * @param {string} content - Original content with YAML frontmatter
+   * @param {string} skillName - Skill name (must match directory name)
+   * @returns {string} Transformed content
+   */
+  transformToSkillFormat(content, skillName) {
+    // Parse frontmatter
+    const fmMatch = content.match(/^---\r?\n([\s\S]*?)\r?\n---\r?\n?([\s\S]*)$/);
+    if (!fmMatch) {
+      // No frontmatter -- wrap with minimal frontmatter
+      const fm = yaml.stringify({ name: skillName, description: skillName }).trimEnd();
+      return `---\n${fm}\n---\n\n${content}`;
+    }
+
+    const frontmatter = fmMatch[1];
+    const body = fmMatch[2];
+
+    // Parse frontmatter with yaml library to handle all quoting variants
+    let description;
+    try {
+      const parsed = yaml.parse(frontmatter);
+      description = parsed?.description || `${skillName} skill`;
+    } catch {
+      description = `${skillName} skill`;
+    }
+
+    // Build new frontmatter with only skills-spec fields, let yaml handle quoting
+    const newFrontmatter = yaml.stringify({ name: skillName, description }).trimEnd();
+    return `---\n${newFrontmatter}\n---\n${body}`;
+  }
+
+  /**
+   * Detect Codex installation by checking for BMAD skills
    */
   async detect(projectDir) {
     // Check both global and project-specific locations
-    const globalDir = this.getCodexPromptDir(null, 'global');
+    const globalDir = this.getCodexSkillsDir(null, 'global');
     const projectDir_local = projectDir || process.cwd();
-    const projectSpecificDir = this.getCodexPromptDir(projectDir_local, 'project');
+    const projectSpecificDir = this.getCodexSkillsDir(projectDir_local, 'project');
 
     // Check global location
     if (await fs.pathExists(globalDir)) {
@@ -240,27 +317,20 @@ class CodexSetup extends BaseIdeSetup {
     };
   }
 
-  getCodexPromptDir(projectDir = null, location = 'global') {
+  getCodexSkillsDir(projectDir = null, location = 'project') {
     if (location === 'project' && projectDir) {
-      return path.join(projectDir, '.codex', 'prompts');
+      return path.join(projectDir, '.agents', 'skills');
     }
-    return path.join(os.homedir(), '.codex', 'prompts');
+    if (location === 'project' && !projectDir) {
+      throw new Error('projectDir is required for project-scoped skill installation');
+    }
+    return path.join(os.homedir(), '.agents', 'skills');
   }
 
-  async flattenAndWriteArtifacts(artifacts, destDir) {
-    let written = 0;
-
-    for (const artifact of artifacts) {
-      const flattenedName = this.flattenFilename(artifact.relativePath);
-      const targetPath = path.join(destDir, flattenedName);
-      await fs.writeFile(targetPath, artifact.content);
-      written++;
-    }
-
-    return written;
-  }
-
-  async clearOldBmadFiles(destDir, options = {}) {
+  /**
+   * Remove existing BMAD skill directories from the skills directory.
+   */
+  async clearOldBmadSkills(destDir, options = {}) {
     if (!(await fs.pathExists(destDir))) {
       return;
     }
@@ -299,7 +369,8 @@ class CodexSetup extends BaseIdeSetup {
   }
 
   async readAndProcessWithProject(filePath, metadata, projectDir) {
-    const content = await fs.readFile(filePath, 'utf8');
+    const rawContent = await fs.readFile(filePath, 'utf8');
+    const content = rawContent.replaceAll('\r\n', '\n').replaceAll('\r', '\n');
     return super.processContent(content, metadata, projectDir);
   }
 
@@ -311,14 +382,14 @@ class CodexSetup extends BaseIdeSetup {
     const lines = [
       'IMPORTANT: Codex Configuration',
       '',
-      '/prompts installed globally to your HOME DIRECTORY.',
+      'Skills installed globally to your HOME DIRECTORY ($HOME/.agents/skills).',
       '',
-      'These prompts reference a specific _bmad path.',
+      'These skills reference a specific _bmad path.',
       "To use with other projects, you'd need to copy the _bmad dir.",
       '',
-      'You can now use /commands in Codex CLI',
-      '  Example: /bmad_bmm_pm',
-      '  Type / to see all available commands',
+      'Skills are available in Codex CLI automatically.',
+      '  Use /skills to see available skills',
+      '  Skills can also be invoked implicitly based on task description',
     ];
     return lines.join('\n');
   }
@@ -330,40 +401,15 @@ class CodexSetup extends BaseIdeSetup {
    * @returns {string} Instructions text
    */
   getProjectSpecificInstructions(projectDir = null, destDir = null) {
-    const isWindows = os.platform() === 'win32';
-
-    const commonLines = [
+    const lines = [
       'Project-Specific Codex Configuration',
       '',
-      `Prompts will be installed to: ${destDir || '<project>/.codex/prompts'}`,
-      '',
-      'REQUIRED: You must set CODEX_HOME to use these prompts',
+      `Skills installed to: ${destDir || '<project>/.agents/skills'}`,
       '',
+      'Codex automatically discovers skills in .agents/skills/ at and above the current directory and in your home directory.',
+      'No additional configuration is needed.',
     ];
 
-    const windowsLines = [
-      'Create a codex.cmd file in your project root:',
-      '',
-      '  @echo off',
-      '  set CODEX_HOME=%~dp0.codex',
-      '  codex %*',
-      '',
-      String.raw`Then run: .\codex instead of codex`,
-      '(The %~dp0 gets the directory of the .cmd file)',
-    ];
-
-    const unixLines = [
-      'Add this alias to your ~/.bashrc or ~/.zshrc:',
-      '',
-      '  alias codex=\'CODEX_HOME="$PWD/.codex" codex\'',
-      '',
-      'After adding, run: source ~/.bashrc  (or source ~/.zshrc)',
-      '(The $PWD uses your current working directory)',
-    ];
-    const closingLines = ['', 'This tells Codex CLI to use prompts from this project instead of ~/.codex'];
-
-    const lines = [...commonLines, ...(isWindows ? windowsLines : unixLines), ...closingLines];
-
     return lines.join('\n');
   }
 
@@ -372,31 +418,34 @@ class CodexSetup extends BaseIdeSetup {
    */
   async cleanup(projectDir = null) {
     // Clean both global and project-specific locations
-    const globalDir = this.getCodexPromptDir(null, 'global');
-    await this.clearOldBmadFiles(globalDir);
+    const globalDir = this.getCodexSkillsDir(null, 'global');
+    await this.clearOldBmadSkills(globalDir);
 
     if (projectDir) {
-      const projectSpecificDir = this.getCodexPromptDir(projectDir, 'project');
-      await this.clearOldBmadFiles(projectSpecificDir);
+      const projectSpecificDir = this.getCodexSkillsDir(projectDir, 'project');
+      await this.clearOldBmadSkills(projectSpecificDir);
     }
   }
 
   /**
-   * Install a custom agent launcher for Codex
-   * @param {string} projectDir - Project directory (not used, Codex installs to home)
+   * Install a custom agent launcher for Codex as an Agent Skill
+   * @param {string} projectDir - Project directory
    * @param {string} agentName - Agent name (e.g., "fred-commit-poet")
    * @param {string} agentPath - Path to compiled agent (relative to project root)
    * @param {Object} metadata - Agent metadata
-   * @returns {Object|null} Info about created command
+   * @returns {Object|null} Info about created skill
    */
   async installCustomAgentLauncher(projectDir, agentName, agentPath, metadata) {
-    const destDir = this.getCodexPromptDir(projectDir, 'project');
-    await fs.ensureDir(destDir);
+    const destDir = this.getCodexSkillsDir(projectDir, 'project');
 
-    const launcherContent = `---
-name: '${agentName}'
-description: '${agentName} agent'
-disable-model-invocation: true
+    // Skill name from the dash name (without .md)
+    const skillName = customAgentDashName(agentName).replace(/\.md$/, '');
+    const skillDir = path.join(destDir, skillName);
+    await fs.ensureDir(skillDir);
+
+    const fm = yaml.stringify({ name: skillName, description: `${agentName} agent` }).trimEnd();
+    const skillContent = `---
+${fm}
 ---
 
 You must fully embody this agent's persona and follow all activation instructions exactly as specified. NEVER break character until given an exit command.
@@ -411,14 +460,12 @@ You must fully embody this agent's persona and follow all activation instruction
 </agent-activation>
 `;
 
-    // Use underscore format: bmad_custom_fred-commit-poet.md
-    const fileName = customAgentDashName(agentName);
-    const launcherPath = path.join(destDir, fileName);
-    await fs.writeFile(launcherPath, launcherContent, 'utf8');
+    const skillPath = path.join(skillDir, 'SKILL.md');
+    await fs.writeFile(skillPath, skillContent, 'utf8');
 
     return {
-      path: path.relative(projectDir, launcherPath),
-      command: `/${fileName.replace('.md', '')}`,
+      path: path.relative(projectDir, skillPath),
+      command: `$${skillName}`,
     };
   }
 }

tools/cli/installers/lib/ide/github-copilot.js

@@ -1,6 +1,6 @@
 const path = require('node:path');
 const { BaseIdeSetup } = require('./_base-ide');
-const chalk = require('chalk');
+const prompts = require('../../../lib/prompts');
 const { AgentCommandGenerator } = require('./shared/agent-command-generator');
 const { BMAD_FOLDER_NAME, toDashPath } = require('./shared/path-utils');
 const fs = require('fs-extra');
@@ -31,7 +31,7 @@ class GitHubCopilotSetup extends BaseIdeSetup {
    * @param {Object} options - Setup options
    */
   async setup(projectDir, bmadDir, options = {}) {
-    console.log(chalk.cyan(`Setting up ${this.name}...`));
+    if (!options.silent) await prompts.log.info(`Setting up ${this.name}...`);
 
     // Create .github/agents and .github/prompts directories
     const githubDir = path.join(projectDir, this.githubDir);
@@ -66,21 +66,15 @@ class GitHubCopilotSetup extends BaseIdeSetup {
       const targetPath = path.join(agentsDir, fileName);
       await this.writeFile(targetPath, agentContent);
       agentCount++;
-
-      console.log(chalk.green(`  ✓ Created agent: ${fileName}`));
     }
 
     // Generate prompt files from bmad-help.csv
     const promptCount = await this.generatePromptFiles(projectDir, bmadDir, agentArtifacts, agentManifest);
 
     // Generate copilot-instructions.md
-    await this.generateCopilotInstructions(projectDir, bmadDir, agentManifest);
+    await this.generateCopilotInstructions(projectDir, bmadDir, agentManifest, options);
 
-    console.log(chalk.green(`\n✓ ${this.name} configured:`));
-    console.log(chalk.dim(`  - ${agentCount} agents created in .github/agents/`));
-    console.log(chalk.dim(`  - ${promptCount} prompts created in .github/prompts/`));
-    console.log(chalk.dim(`  - copilot-instructions.md generated`));
-    console.log(chalk.dim(`  - Destination: .github/`));
+    if (!options.silent) await prompts.log.success(`${this.name} configured: ${agentCount} agents, ${promptCount} prompts → .github/`);
 
     return {
       success: true,
@@ -406,7 +400,7 @@ tools: ${toolsStr}
    * @param {string} bmadDir - BMAD installation directory
    * @param {Map} agentManifest - Agent manifest data
    */
-  async generateCopilotInstructions(projectDir, bmadDir, agentManifest) {
+  async generateCopilotInstructions(projectDir, bmadDir, agentManifest, options = {}) {
     const configVars = await this.loadModuleConfig(bmadDir);
 
     // Build the agents table from the manifest
@@ -495,19 +489,16 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
         const after = existing.slice(endIdx + markerEnd.length);
         const merged = `${before}${markedContent}${after}`;
         await this.writeFile(instructionsPath, merged);
-        console.log(chalk.green('  ✓ Updated BMAD section in copilot-instructions.md'));
       } else {
         // Existing file without markers — back it up before overwriting
         const backupPath = `${instructionsPath}.bak`;
         await fs.copy(instructionsPath, backupPath);
-        console.log(chalk.yellow(`  ⚠ Backed up existing copilot-instructions.md → copilot-instructions.md.bak`));
+        if (!options.silent) await prompts.log.warn(`  Backed up copilot-instructions.md → .bak`);
         await this.writeFile(instructionsPath, `${markedContent}\n`);
-        console.log(chalk.green('  ✓ Generated copilot-instructions.md (with BMAD markers)'));
       }
     } else {
       // No existing file — create fresh with markers
       await this.writeFile(instructionsPath, `${markedContent}\n`);
-      console.log(chalk.green('  ✓ Generated copilot-instructions.md'));
     }
   }
 
@@ -607,7 +598,7 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
   /**
    * Cleanup GitHub Copilot configuration - surgically remove only BMAD files
    */
-  async cleanup(projectDir) {
+  async cleanup(projectDir, options = {}) {
     // Clean up agents directory
     const agentsDir = path.join(projectDir, this.githubDir, this.agentsDir);
     if (await fs.pathExists(agentsDir)) {
@@ -621,8 +612,8 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
         }
       }
 
-      if (removed > 0) {
-        console.log(chalk.dim(`  Cleaned up ${removed} existing BMAD agents`));
+      if (removed > 0 && !options.silent) {
+        await prompts.log.message(`  Cleaned up ${removed} existing BMAD agents`);
       }
     }
 
@@ -639,16 +630,70 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
         }
       }
 
-      if (removed > 0) {
-        console.log(chalk.dim(`  Cleaned up ${removed} existing BMAD prompts`));
+      if (removed > 0 && !options.silent) {
+        await prompts.log.message(`  Cleaned up ${removed} existing BMAD prompts`);
       }
     }
 
-    // Note: copilot-instructions.md is NOT cleaned up here.
-    // generateCopilotInstructions() handles marker-based replacement in a single
-    // read-modify-write pass, which correctly preserves user content outside the markers.
-    // Stripping markers here would cause generation to treat the file as legacy (no markers)
-    // and overwrite user content.
+    // During uninstall, also strip BMAD markers from copilot-instructions.md.
+    // During reinstall (default), this is skipped because generateCopilotInstructions()
+    // handles marker-based replacement in a single read-modify-write pass,
+    // which correctly preserves user content outside the markers.
+    if (options.isUninstall) {
+      await this.cleanupCopilotInstructions(projectDir, options);
+    }
+  }
+
+  /**
+   * Strip BMAD marker section from copilot-instructions.md
+   * If file becomes empty after stripping, delete it.
+   * If a .bak backup exists and the main file was deleted, restore the backup.
+   * @param {string} projectDir - Project directory
+   * @param {Object} [options] - Options (e.g. { silent: true })
+   */
+  async cleanupCopilotInstructions(projectDir, options = {}) {
+    const instructionsPath = path.join(projectDir, this.githubDir, 'copilot-instructions.md');
+    const backupPath = `${instructionsPath}.bak`;
+
+    if (!(await fs.pathExists(instructionsPath))) {
+      return;
+    }
+
+    const content = await fs.readFile(instructionsPath, 'utf8');
+    const markerStart = '<!-- BMAD:START -->';
+    const markerEnd = '<!-- BMAD:END -->';
+    const startIdx = content.indexOf(markerStart);
+    const endIdx = content.indexOf(markerEnd);
+
+    if (startIdx === -1 || endIdx === -1 || endIdx <= startIdx) {
+      return; // No valid markers found
+    }
+
+    // Strip the marker section (including markers)
+    const before = content.slice(0, startIdx);
+    const after = content.slice(endIdx + markerEnd.length);
+    const cleaned = before + after;
+
+    if (cleaned.trim().length === 0) {
+      // File is empty after stripping — delete it
+      await fs.remove(instructionsPath);
+
+      // If backup exists, restore it
+      if (await fs.pathExists(backupPath)) {
+        await fs.rename(backupPath, instructionsPath);
+        if (!options.silent) {
+          await prompts.log.message('  Restored copilot-instructions.md from backup');
+        }
+      }
+    } else {
+      // Write cleaned content back (preserve original whitespace)
+      await fs.writeFile(instructionsPath, cleaned, 'utf8');
+
+      // If backup exists, it's stale now — remove it
+      if (await fs.pathExists(backupPath)) {
+        await fs.remove(backupPath);
+      }
+    }
   }
 }
 

tools/cli/installers/lib/ide/manager.js

@@ -216,13 +216,14 @@ class IdeManager {
   /**
    * Cleanup IDE configurations
    * @param {string} projectDir - Project directory
+   * @param {Object} [options] - Cleanup options passed through to handlers
    */
-  async cleanup(projectDir) {
+  async cleanup(projectDir, options = {}) {
     const results = [];
 
     for (const [name, handler] of this.handlers) {
       try {
-        await handler.cleanup(projectDir);
+        await handler.cleanup(projectDir, options);
         results.push({ ide: name, success: true });
       } catch (error) {
         results.push({ ide: name, success: false, error: error.message });
@@ -232,6 +233,40 @@ class IdeManager {
     return results;
   }
 
+  /**
+   * Cleanup only the IDEs in the provided list
+   * Falls back to cleanup() (all handlers) if ideList is empty or undefined
+   * @param {string} projectDir - Project directory
+   * @param {Array<string>} ideList - List of IDE names to clean up
+   * @param {Object} [options] - Cleanup options passed through to handlers
+   * @returns {Array} Results array
+   */
+  async cleanupByList(projectDir, ideList, options = {}) {
+    if (!ideList || ideList.length === 0) {
+      return this.cleanup(projectDir, options);
+    }
+
+    await this.ensureInitialized();
+    const results = [];
+
+    // Build lowercase lookup for case-insensitive matching
+    const lowercaseHandlers = new Map([...this.handlers.entries()].map(([k, v]) => [k.toLowerCase(), v]));
+
+    for (const ideName of ideList) {
+      const handler = lowercaseHandlers.get(ideName.toLowerCase());
+      if (!handler) continue;
+
+      try {
+        await handler.cleanup(projectDir, options);
+        results.push({ ide: ideName, success: true });
+      } catch (error) {
+        results.push({ ide: ideName, success: false, error: error.message });
+      }
+    }
+
+    return results;
+  }
+
   /**
    * Get list of supported IDEs
    * @returns {Array} List of supported IDE names