docs/_STYLE_GUIDE.md

@@ -78,6 +78,7 @@ your-project/
 ├── _bmad/                         # BMad configuration
 ├── _bmad-output/
 │   ├── PRD.md                     # Your requirements document
+│   └── bmm-workflow-status.yaml   # Progress tracking
 └── ...
 ```
 ````
@@ -142,7 +143,7 @@ your-project/
 ### Types
 
 | Type              | Example                      |
-| ----------------- | ----------------------------- |
+| ----------------- | ---------------------------- |
 | **Index/Landing** | `core-concepts/index.md`     |
 | **Concept**       | `what-are-agents.md`         |
 | **Feature**       | `quick-flow.md`              |

package.json

@@ -25,7 +25,6 @@
   },
   "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",

src/bmm/workflows/document-project/instructions.md

@@ -8,7 +8,55 @@
 
 <critical>This router determines workflow mode and delegates to specialized sub-workflows</critical>
 
-<step n="1" goal="Check for ability to resume and determine workflow mode">
+<step n="1" goal="Validate workflow and get project info">
+
+<invoke-workflow path="{project-root}/_bmad/bmm/workflows/workflow-status">
+  <param>mode: data</param>
+  <param>data_request: project_config</param>
+</invoke-workflow>
+
+<check if="status_exists == false">
+  <output>{{suggestion}}</output>
+  <output>Note: Documentation workflow can run standalone. Continuing without progress tracking.</output>
+  <action>Set standalone_mode = true</action>
+  <action>Set status_file_found = false</action>
+</check>
+
+<check if="status_exists == true">
+  <action>Store {{status_file_path}} for later updates</action>
+  <action>Set status_file_found = true</action>
+
+  <!-- Extract brownfield/greenfield from status data -->
+  <check if="field_type == 'greenfield'">
+    <output>Note: This is a greenfield project. Documentation workflow is typically for brownfield projects.</output>
+    <ask>Continue anyway to document planning artifacts? (y/n)</ask>
+    <check if="n">
+      <action>Exit workflow</action>
+    </check>
+  </check>
+
+  <!-- Now validate sequencing -->
+  <invoke-workflow path="{project-root}/_bmad/bmm/workflows/workflow-status">
+    <param>mode: validate</param>
+    <param>calling_workflow: document-project</param>
+  </invoke-workflow>
+
+  <check if="warning != ''">
+    <output>{{warning}}</output>
+    <output>Note: This may be auto-invoked by prd for brownfield documentation.</output>
+    <ask>Continue with documentation? (y/n)</ask>
+    <check if="n">
+      <output>{{suggestion}}</output>
+      <action>Exit workflow</action>
+    </check>
+  </check>
+</check>
+
+</step>
+
+<step n="2" goal="Check for resumability and determine workflow mode">
+<critical>SMART LOADING STRATEGY: Check state file FIRST before loading any CSV files</critical>
+
 <action>Check for existing state file at: {project_knowledge}/project-scan-report.json</action>
 
 <check if="project-scan-report.json exists">
@@ -127,4 +175,47 @@ Your choice [1/2/3]:
 
 </step>
 
+<step n="4" goal="Update status and complete">
+
+<check if="status_file_found == true">
+  <invoke-workflow path="{project-root}/_bmad/bmm/workflows/workflow-status">
+    <param>mode: update</param>
+    <param>action: complete_workflow</param>
+    <param>workflow_name: document-project</param>
+  </invoke-workflow>
+
+  <check if="success == true">
+    <output>Status updated!</output>
+  </check>
+</check>
+
+<output>**✅ Document Project Workflow Complete, {user_name}!**
+
+**Documentation Generated:**
+
+- Mode: {{workflow_mode}}
+- Scan Level: {{scan_level}}
+- Output: {project_knowledge}/index.md and related files
+
+{{#if status_file_found}}
+**Status Updated:**
+
+- Progress tracking updated
+
+**Next Steps:**
+
+- **Next required:** {{next_workflow}} ({{next_agent}} agent)
+
+Check status anytime with: `workflow-status`
+{{else}}
+**Next Steps:**
+Since no workflow is in progress:
+
+- Refer to the BMM workflow guide if unsure what to do next
+- Or run `workflow-init` to create a workflow path and get guided next steps
+  {{/if}}
+  </output>
+
+</step>
+
 </workflow>

tools/cli/README.md

@@ -16,8 +16,8 @@ Always displayed after the module is configured:
 
 ```yaml
 post-install-notes: |
-  Thank you for choosing the XYZ Cool Module
+  Remember to set the API_KEY environment variable.
-  For Support about this Module call 555-1212
+  See: https://example.com/setup
 ```
 
 ### Conditional Format

tools/cli/commands/uninstall.js

@@ -1,167 +0,0 @@
-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/blob/main/CHANGELOG.md
+  Latest updates: https://github.com/bmad-code-org/BMAD-METHOD/CHANGELOG.md
 
   ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━
 

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

@@ -527,13 +527,8 @@ class Installer {
             const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
 
             for (const cachedModule of cachedModules) {
+              if (cachedModule.isDirectory()) {
                 const moduleId = cachedModule.name;
-              const cachedPath = path.join(cacheDir, moduleId);
-
-              // Skip if path doesn't exist (broken symlink, deleted dir) - avoids lstat ENOENT
-              if (!(await fs.pathExists(cachedPath)) || !cachedModule.isDirectory()) {
-                continue;
-              }
 
                 // Skip if we already have this module from manifest
                 if (customModulePaths.has(moduleId)) {
@@ -547,12 +542,15 @@ class Installer {
                   continue;
                 }
 
+                const cachedPath = path.join(cacheDir, moduleId);
+
                 // Check if this is actually a custom module (has module.yaml)
                 const moduleYamlPath = path.join(cachedPath, 'module.yaml');
                 if (await fs.pathExists(moduleYamlPath)) {
                   customModulePaths.set(moduleId, cachedPath);
                 }
               }
+            }
 
             // Update module manager with the new custom module paths from cache
             this.moduleManager.setCustomModulePaths(customModulePaths);
@@ -611,13 +609,8 @@ class Installer {
           const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
 
           for (const cachedModule of cachedModules) {
+            if (cachedModule.isDirectory()) {
               const moduleId = cachedModule.name;
-            const cachedPath = path.join(cacheDir, moduleId);
-
-            // Skip if path doesn't exist (broken symlink, deleted dir) - avoids lstat ENOENT
-            if (!(await fs.pathExists(cachedPath)) || !cachedModule.isDirectory()) {
-              continue;
-            }
 
               // Skip if we already have this module from manifest
               if (customModulePaths.has(moduleId)) {
@@ -631,12 +624,15 @@ class Installer {
                 continue;
               }
 
+              const cachedPath = path.join(cacheDir, moduleId);
+
               // Check if this is actually a custom module (has module.yaml)
               const moduleYamlPath = path.join(cachedPath, 'module.yaml');
               if (await fs.pathExists(moduleYamlPath)) {
                 customModulePaths.set(moduleId, cachedPath);
               }
             }
+          }
 
           // Update module manager with the new custom module paths from cache
           this.moduleManager.setCustomModulePaths(customModulePaths);
@@ -953,11 +949,12 @@ class Installer {
               if (!isCustomModule && config._customModuleSources && config._customModuleSources.has(moduleName)) {
                 customInfo = config._customModuleSources.get(moduleName);
                 isCustomModule = true;
-                if (customInfo.sourcePath && !customInfo.path) {
+                if (
-                  customInfo.path = path.isAbsolute(customInfo.sourcePath)
+                  customInfo.sourcePath &&
-                    ? customInfo.sourcePath
+                  (customInfo.sourcePath.startsWith('_config') || customInfo.sourcePath.includes('_config/custom')) &&
-                    : path.join(bmadDir, customInfo.sourcePath);
+                  !customInfo.path
-                }
+                )
+                  customInfo.path = customInfo.sourcePath;
               }
 
               // Finally check regular custom content
@@ -1531,157 +1528,20 @@ class Installer {
   }
 
   /**
-   * Uninstall BMAD with selective removal options
+   * Uninstall BMAD
-   * @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, options = {}) {
+  async uninstall(directory) {
     const projectDir = path.resolve(directory);
     const { bmadDir } = await this.findBmadDir(projectDir);
 
-    if (!(await fs.pathExists(bmadDir))) {
-      return { success: false, reason: 'not-installed' };
-    }
-
-    // 1. DETECT: Read state BEFORE deleting anything
-    const existingInstall = await this.detector.detect(bmadDir);
-    const outputFolder = await this._readOutputFolder(bmadDir);
-
-    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;
     }
 
-  /**
+    // Clean up IDE configurations
-   * Get the configured output folder name for a project
+    await this.ideManager.cleanup(projectDir);
-   * 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);
-  }
 
-  /**
+    return { success: true };
-   * 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';
   }
 
   /**
@@ -2376,35 +2236,15 @@ class Installer {
       const configuredIdes = existingInstall.ides || [];
       const projectRoot = path.dirname(bmadDir);
 
-      // Get custom module sources: first from --custom-content (re-cache from source), then from cache
+      // Get custom module sources from cache
       const customModuleSources = new Map();
-      if (config.customContent?.sources?.length > 0) {
-        for (const source of config.customContent.sources) {
-          if (source.id && source.path && (await fs.pathExists(source.path))) {
-            customModuleSources.set(source.id, {
-              id: source.id,
-              name: source.name || source.id,
-              sourcePath: source.path,
-              cached: false, // From CLI, will be re-cached
-            });
-          }
-        }
-      }
       const cacheDir = path.join(bmadDir, '_config', 'custom');
       if (await fs.pathExists(cacheDir)) {
         const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
 
         for (const cachedModule of cachedModules) {
+          if (cachedModule.isDirectory()) {
             const moduleId = cachedModule.name;
-          const cachedPath = path.join(cacheDir, moduleId);
-
-          // Skip if path doesn't exist (broken symlink, deleted dir) - avoids lstat ENOENT
-          if (!(await fs.pathExists(cachedPath))) {
-            continue;
-          }
-          if (!cachedModule.isDirectory()) {
-            continue;
-          }
 
             // Skip if we already have this module from manifest
             if (customModuleSources.has(moduleId)) {
@@ -2418,6 +2258,8 @@ class Installer {
               continue;
             }
 
+            const cachedPath = path.join(cacheDir, moduleId);
+
             // Check if this is actually a custom module (has module.yaml)
             const moduleYamlPath = path.join(cachedPath, 'module.yaml');
             if (await fs.pathExists(moduleYamlPath)) {
@@ -2431,6 +2273,7 @@ class Installer {
             }
           }
         }
+      }
 
       // Load saved IDE configurations
       const savedIdeConfigs = await this.ideConfigManager.loadAllIdeConfigs(bmadDir);
@@ -2564,7 +2407,6 @@ class Installer {
         _savedIdeConfigs: savedIdeConfigs, // Pass saved IDE configs to installer
         _customModuleSources: customModuleSources, // Pass custom module sources for updates
         _existingModules: installedModules, // Pass all installed modules for manifest generation
-        customContent: config.customContent, // Pass through for re-caching from source
       };
 
       // Call the standard install method

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

@@ -456,18 +456,8 @@ 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);
@@ -519,41 +509,6 @@ 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/github-copilot.js

@@ -1,6 +1,6 @@
 const path = require('node:path');
 const { BaseIdeSetup } = require('./_base-ide');
-const prompts = require('../../../lib/prompts');
+const chalk = require('chalk');
 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 = {}) {
-    if (!options.silent) await prompts.log.info(`Setting up ${this.name}...`);
+    console.log(chalk.cyan(`Setting up ${this.name}...`));
 
     // Create .github/agents and .github/prompts directories
     const githubDir = path.join(projectDir, this.githubDir);
@@ -66,15 +66,21 @@ 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, options);
+    await this.generateCopilotInstructions(projectDir, bmadDir, agentManifest);
 
-    if (!options.silent) await prompts.log.success(`${this.name} configured: ${agentCount} agents, ${promptCount} prompts → .github/`);
+    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/`));
 
     return {
       success: true,
@@ -400,7 +406,7 @@ tools: ${toolsStr}
    * @param {string} bmadDir - BMAD installation directory
    * @param {Map} agentManifest - Agent manifest data
    */
-  async generateCopilotInstructions(projectDir, bmadDir, agentManifest, options = {}) {
+  async generateCopilotInstructions(projectDir, bmadDir, agentManifest) {
     const configVars = await this.loadModuleConfig(bmadDir);
 
     // Build the agents table from the manifest
@@ -489,16 +495,19 @@ 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);
-        if (!options.silent) await prompts.log.warn(`  Backed up copilot-instructions.md → .bak`);
+        console.log(chalk.yellow(`  ⚠ Backed up existing copilot-instructions.md → 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'));
     }
   }
 
@@ -598,7 +607,7 @@ 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, options = {}) {
+  async cleanup(projectDir) {
     // Clean up agents directory
     const agentsDir = path.join(projectDir, this.githubDir, this.agentsDir);
     if (await fs.pathExists(agentsDir)) {
@@ -612,8 +621,8 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
         }
       }
 
-      if (removed > 0 && !options.silent) {
+      if (removed > 0) {
-        await prompts.log.message(`  Cleaned up ${removed} existing BMAD agents`);
+        console.log(chalk.dim(`  Cleaned up ${removed} existing BMAD agents`));
       }
     }
 
@@ -630,70 +639,16 @@ Type \`/bmad-\` in Copilot Chat to see all available BMAD workflows and agent ac
         }
       }
 
-      if (removed > 0 && !options.silent) {
+      if (removed > 0) {
-        await prompts.log.message(`  Cleaned up ${removed} existing BMAD prompts`);
+        console.log(chalk.dim(`  Cleaned up ${removed} existing BMAD prompts`));
       }
     }
 
-    // During uninstall, also strip BMAD markers from copilot-instructions.md.
+    // Note: copilot-instructions.md is NOT cleaned up here.
-    // During reinstall (default), this is skipped because generateCopilotInstructions()
+    // generateCopilotInstructions() handles marker-based replacement in a single
-    // handles marker-based replacement in a single read-modify-write pass,
+    // read-modify-write pass, which correctly preserves user content outside the markers.
-    // which correctly preserves user content outside the markers.
+    // Stripping markers here would cause generation to treat the file as legacy (no markers)
-    if (options.isUninstall) {
+    // and overwrite user content.
-      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

@@ -216,14 +216,13 @@ class IdeManager {
   /**
    * Cleanup IDE configurations
    * @param {string} projectDir - Project directory
-   * @param {Object} [options] - Cleanup options passed through to handlers
    */
-  async cleanup(projectDir, options = {}) {
+  async cleanup(projectDir) {
     const results = [];
 
     for (const [name, handler] of this.handlers) {
       try {
-        await handler.cleanup(projectDir, options);
+        await handler.cleanup(projectDir);
         results.push({ ide: name, success: true });
       } catch (error) {
         results.push({ ide: name, success: false, error: error.message });
@@ -233,40 +232,6 @@ 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

tools/cli/lib/ui.js

@@ -245,48 +245,11 @@ class UI {
 
       // Handle quick update separately
       if (actionType === 'quick-update') {
-        // Pass --custom-content through so installer can re-cache if cache is missing
+        // Quick update doesn't install custom content - just updates existing modules
-        let customContentForQuickUpdate = { hasCustomContent: false };
-        if (options.customContent) {
-          const paths = options.customContent
-            .split(',')
-            .map((p) => p.trim())
-            .filter(Boolean);
-          if (paths.length > 0) {
-            const customPaths = [];
-            const selectedModuleIds = [];
-            const sources = [];
-            for (const customPath of paths) {
-              const expandedPath = this.expandUserPath(customPath);
-              const validation = this.validateCustomContentPathSync(expandedPath);
-              if (validation) continue;
-              let moduleMeta;
-              try {
-                const moduleYamlPath = path.join(expandedPath, 'module.yaml');
-                moduleMeta = require('yaml').parse(await fs.readFile(moduleYamlPath, 'utf-8'));
-              } catch {
-                continue;
-              }
-              if (!moduleMeta?.code) continue;
-              customPaths.push(expandedPath);
-              selectedModuleIds.push(moduleMeta.code);
-              sources.push({ path: expandedPath, id: moduleMeta.code, name: moduleMeta.name || moduleMeta.code });
-            }
-            if (customPaths.length > 0) {
-              customContentForQuickUpdate = {
-                hasCustomContent: true,
-                selected: true,
-                sources,
-                selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
-                selectedModuleIds,
-              };
-            }
-          }
-        }
         return {
           actionType: 'quick-update',
           directory: confirmedDirectory,
-          customContent: customContentForQuickUpdate,
+          customContent: { hasCustomContent: false },
           skipPrompts: options.yes || false,
         };
       }
@@ -364,11 +327,6 @@ class UI {
               continue;
             }
 
-            if (!moduleMeta) {
-              await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml is empty`);
-              continue;
-            }
-
             if (!moduleMeta.code) {
               await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml missing 'code' field`);
               continue;
@@ -388,10 +346,11 @@ class UI {
               selectedCustomModules: selectedModuleIds,
               customContentConfig: {
                 hasCustomContent: true,
-                selected: true,
+                paths: customPaths,
-                sources,
-                selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
                 selectedModuleIds: selectedModuleIds,
+                sources,
+                selected: true,
+                selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
               },
             };
           }
@@ -518,11 +477,6 @@ class UI {
           continue;
         }
 
-        if (!moduleMeta) {
-          await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml is empty`);
-          continue;
-        }
-
         if (!moduleMeta.code) {
           await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml missing 'code' field`);
           continue;
@@ -540,10 +494,11 @@ class UI {
       if (customPaths.length > 0) {
         customContentConfig = {
           hasCustomContent: true,
-          selected: true,
+          paths: customPaths,
-          sources,
-          selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
           selectedModuleIds: selectedModuleIds,
+          sources,
+          selected: true,
+          selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
         };
       }
     } else if (!options.yes) {