bmad-method 6.0.0-alpha.2 → 6.0.0-alpha.20

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

@@ -2,6 +2,7 @@ const path = require('node:path');
 const fs = require('fs-extra');
 const chalk = require('chalk');
 const ora = require('ora');
+const inquirer = require('inquirer');
 const { Detector } = require('./detector');
 const { Manifest } = require('./manifest');
 const { ModuleManager } = require('../modules/manager');
@@ -11,12 +12,14 @@ const { Config } = require('../../../lib/config');
 const { XmlHandler } = require('../../../lib/xml-handler');
 const { DependencyResolver } = require('./dependency-resolver');
 const { ConfigCollector } = require('./config-collector');
-// processInstallation no longer needed - LLMs understand {project-root}
 const { getProjectRoot, getSourcePath, getModulePath } = require('../../../lib/project-root');
-const { AgentPartyGenerator } = require('../../../lib/agent-party-generator');
 const { CLIUtils } = require('../../../lib/cli-utils');
 const { ManifestGenerator } = require('./manifest-generator');
 const { IdeConfigManager } = require('./ide-config-manager');
+const { CustomHandler } = require('../custom/handler');
+
+// BMAD installation folder name - this is constant and should never change
+const BMAD_FOLDER_NAME = '_bmad';
 
 class Installer {
   constructor() {
@@ -30,7 +33,206 @@ class Installer {
     this.dependencyResolver = new DependencyResolver();
     this.configCollector = new ConfigCollector();
     this.ideConfigManager = new IdeConfigManager();
-    this.installedFiles = []; // Track all installed files
+    this.installedFiles = new Set(); // Track all installed files
+    this.ttsInjectedFiles = []; // Track files with TTS injection applied
+    this.bmadFolderName = BMAD_FOLDER_NAME;
+  }
+
+  /**
+   * Find the bmad installation directory in a project
+   * Always uses the standard _bmad folder name
+   * Also checks for legacy _cfg folder for migration
+   * @param {string} projectDir - Project directory
+   * @returns {Promise<Object>} { bmadDir: string, hasLegacyCfg: boolean }
+   */
+  async findBmadDir(projectDir) {
+    const bmadDir = path.join(projectDir, BMAD_FOLDER_NAME);
+
+    // Check if project directory exists
+    if (!(await fs.pathExists(projectDir))) {
+      // Project doesn't exist yet, return default
+      return { bmadDir, hasLegacyCfg: false };
+    }
+
+    // Check for legacy _cfg folder if bmad directory exists
+    let hasLegacyCfg = false;
+    if (await fs.pathExists(bmadDir)) {
+      const legacyCfgPath = path.join(bmadDir, '_cfg');
+      if (await fs.pathExists(legacyCfgPath)) {
+        hasLegacyCfg = true;
+      }
+    }
+
+    return { bmadDir, hasLegacyCfg };
+  }
+
+  /**
+   * @function copyFileWithPlaceholderReplacement
+   * @intent Copy files from BMAD source to installation directory with dynamic content transformation
+   * @why Enables installation-time customization: _bmad replacement + optional AgentVibes TTS injection
+   * @param {string} sourcePath - Absolute path to source file in BMAD repository
+   * @param {string} targetPath - Absolute path to destination file in user's project
+   * @param {string} bmadFolderName - User's chosen bmad folder name (default: 'bmad')
+   * @returns {Promise<void>} Resolves when file copy and transformation complete
+   * @sideeffects Writes transformed file to targetPath, creates parent directories if needed
+   * @edgecases Binary files bypass transformation, falls back to raw copy if UTF-8 read fails
+   * @calledby installCore(), installModule(), IDE installers during file vendoring
+   * @calls processTTSInjectionPoints(), fs.readFile(), fs.writeFile(), fs.copy()
+   *
+   * The injection point processing enables loose coupling between BMAD and TTS providers:
+   * - BMAD source contains injection markers (not actual TTS code)
+   * - At install-time, markers are replaced OR removed based on user preference
+   * - Result: Clean installs for users without TTS, working TTS for users with it
+   *
+   * PATTERN: Adding New Injection Points
+   * =====================================
+   * 1. Add HTML comment marker in BMAD source file:
+   *    <!-- TTS_INJECTION:feature-name -->
+   *
+   * 2. Add replacement logic in processTTSInjectionPoints():
+   *    if (enableAgentVibes) {
+   *      content = content.replace(/<!-- TTS_INJECTION:feature-name -->/g, 'actual code');
+   *    } else {
+   *      content = content.replace(/<!-- TTS_INJECTION:feature-name -->\n?/g, '');
+   *    }
+   *
+   * 3. Document marker in instructions.md (if applicable)
+   */
+  async copyFileWithPlaceholderReplacement(sourcePath, targetPath) {
+    // List of text file extensions that should have placeholder replacement
+    const textExtensions = ['.md', '.yaml', '.yml', '.txt', '.json', '.js', '.ts', '.html', '.css', '.sh', '.bat', '.csv', '.xml'];
+    const ext = path.extname(sourcePath).toLowerCase();
+
+    // Check if this is a text file that might contain placeholders
+    if (textExtensions.includes(ext)) {
+      try {
+        // Read the file content
+        let content = await fs.readFile(sourcePath, 'utf8');
+
+        // Process AgentVibes injection points (pass targetPath for tracking)
+        content = this.processTTSInjectionPoints(content, targetPath);
+
+        // Write to target with replaced content
+        await fs.ensureDir(path.dirname(targetPath));
+        await fs.writeFile(targetPath, content, 'utf8');
+      } catch {
+        // If reading as text fails (might be binary despite extension), fall back to regular copy
+        await fs.copy(sourcePath, targetPath, { overwrite: true });
+      }
+    } else {
+      // Binary file or other file type - just copy directly
+      await fs.copy(sourcePath, targetPath, { overwrite: true });
+    }
+  }
+
+  /**
+   * @function processTTSInjectionPoints
+   * @intent Transform TTS injection markers based on user's installation choice
+   * @why Enables optional TTS integration without tight coupling between BMAD and TTS providers
+   * @param {string} content - Raw file content containing potential injection markers
+   * @returns {string} Transformed content with markers replaced (if enabled) or stripped (if disabled)
+   * @sideeffects None - pure transformation function
+   * @edgecases Returns content unchanged if no markers present, safe to call on all files
+   * @calledby copyFileWithPlaceholderReplacement() during every file copy operation
+   * @calls String.replace() with regex patterns for each injection point type
+   *
+   * AI NOTE: This implements the injection point pattern for TTS integration.
+   * Key architectural decisions:
+   *
+   * 1. **Why Injection Points vs Direct Integration?**
+   *    - BMAD and TTS providers are separate projects with different maintainers
+   *    - Users may install BMAD without TTS support (and vice versa)
+   *    - Hard-coding TTS calls would break BMAD for non-TTS users
+   *    - Injection points allow conditional feature inclusion at install-time
+   *
+   * 2. **How It Works:**
+   *    - BMAD source contains markers: <!-- TTS_INJECTION:feature-name -->
+   *    - During installation, user is prompted: "Enable AgentVibes TTS?"
+   *    - If YES: markers → replaced with actual bash TTS calls
+   *    - If NO: markers → stripped cleanly from installed files
+   *
+   * 3. **State Management:**
+   *    - this.enableAgentVibes set in install() method from config.enableAgentVibes
+   *    - config.enableAgentVibes comes from ui.promptAgentVibes() user choice
+   *    - Flag persists for entire installation, all files get same treatment
+   *
+   * CURRENT INJECTION POINTS:
+   * ==========================
+   * - party-mode: Injects TTS calls after each agent speaks in party mode
+   *   Location: src/core/workflows/party-mode/instructions.md
+   *   Marker: <!-- TTS_INJECTION:party-mode -->
+   *   Replacement: Bash call to .claude/hooks/bmad-speak.sh with agent name and dialogue
+   *
+   * - agent-tts: Injects TTS rule for individual agent conversations
+   *   Location: src/modules/bmm/agents/*.md (all agent files)
+   *   Marker: <!-- TTS_INJECTION:agent-tts -->
+   *   Replacement: Rule instructing agent to call bmad-speak.sh with agent ID and response
+   *
+   * ADDING NEW INJECTION POINTS:
+   * =============================
+   * 1. Add new case in this function:
+   *    content = content.replace(
+   *      /<!-- TTS_INJECTION:new-feature -->/g,
+   *      `code to inject when enabled`
+   *    );
+   *
+   * 2. Add marker to BMAD source file at injection location
+   *
+   * 3. Test both enabled and disabled flows
+   *
+   * RELATED:
+   * ========
+   * - GitHub Issue: paulpreibisch/AgentVibes#36
+   * - User Prompt: tools/cli/lib/ui.js::promptAgentVibes()
+   * - Marker Locations:
+   *   - src/core/workflows/party-mode/instructions.md:101
+   *   - src/modules/bmm/agents/*.md (rules sections)
+   * - TTS Hook: .claude/hooks/bmad-speak.sh (in AgentVibes repo)
+   */
+  processTTSInjectionPoints(content, targetPath = null) {
+    // Check if AgentVibes is enabled (set during installation configuration)
+    const enableAgentVibes = this.enableAgentVibes || false;
+
+    // Check if content contains any TTS injection markers
+    const hasPartyMode = content.includes('<!-- TTS_INJECTION:party-mode -->');
+    const hasAgentTTS = content.includes('<!-- TTS_INJECTION:agent-tts -->');
+
+    if (enableAgentVibes) {
+      // Replace party-mode injection marker with actual TTS call
+      // Use single quotes to prevent shell expansion of special chars like !
+      content = content.replaceAll(
+        '<!-- TTS_INJECTION:party-mode -->',
+        `<critical>IMPORTANT: Always use PROJECT hooks (.claude/hooks/), NEVER global hooks (~/.claude/hooks/)</critical>
+
+        If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
+         - Use Bash tool: \`.claude/hooks/bmad-speak.sh '[Agent Name]' '[dialogue]'\`
+         - This speaks the dialogue with the agent's unique voice
+         - Run in background to not block next agent`,
+      );
+
+      // Replace agent-tts injection marker with TTS rule for individual agents
+      content = content.replaceAll(
+        '<!-- TTS_INJECTION:agent-tts -->',
+        `- When responding to user messages, speak your responses using TTS:
+          Call: \`.claude/hooks/bmad-speak.sh '{agent-id}' '{response-text}'\` after each response
+          Replace {agent-id} with YOUR agent ID from <agent id="..."> tag at top of this file
+          Replace {response-text} with the text you just output to the user
+          IMPORTANT: Use single quotes as shown - do NOT escape special characters like ! or $ inside single quotes
+          Run in background (&) to avoid blocking`,
+      );
+
+      // Track files that had TTS injection applied
+      if (targetPath && (hasPartyMode || hasAgentTTS)) {
+        const injectionType = hasPartyMode ? 'party-mode' : 'agent-tts';
+        this.ttsInjectedFiles.push({ path: targetPath, type: injectionType });
+      }
+    } else {
+      // Strip injection markers cleanly when AgentVibes is disabled
+      content = content.replaceAll(/<!-- TTS_INJECTION:party-mode -->\n?/g, '');
+      content = content.replaceAll(/<!-- TTS_INJECTION:agent-tts -->\n?/g, '');
+    }
+
+    return content;
   }
 
   /**
@@ -61,7 +263,7 @@ class Installer {
     // Check for already configured IDEs
     const { Detector } = require('./detector');
     const detector = new Detector();
-    const bmadDir = path.join(projectDir, 'bmad');
+    const bmadDir = path.join(projectDir, BMAD_FOLDER_NAME);
 
     // During full reinstall, use the saved previous IDEs since bmad dir was deleted
     // Otherwise detect from existing installation
@@ -96,7 +298,10 @@ class Installer {
 
         for (const ide of newlySelectedIdes) {
           // List of IDEs that have interactive prompts
-          const needsPrompts = ['claude-code', 'github-copilot', 'roo', 'cline', 'auggie', 'codex', 'qwen', 'gemini'].includes(ide);
+          //TODO: Why is this here, hardcoding this list here is bad, fix me!
+          const needsPrompts = ['claude-code', 'github-copilot', 'roo', 'cline', 'auggie', 'codex', 'qwen', 'gemini', 'rovo-dev'].includes(
+            ide,
+          );
 
           if (needsPrompts) {
             // Get IDE handler and collect configuration
@@ -117,7 +322,6 @@ class Installer {
               } else if (ideModule.default) {
                 SetupClass = ideModule.default;
               } else {
-                // Skip if no setup class found
                 continue;
               }
 
@@ -163,22 +367,29 @@ class Installer {
    * @param {string[]} config.ides - IDEs to configure
    * @param {boolean} config.skipIde - Skip IDE configuration
    */
-  async install(config) {
-    // Display BMAD logo
-    CLIUtils.displayLogo();
+  async install(originalConfig) {
+    // Clone config to avoid mutating the caller's object
+    const config = { ...originalConfig };
 
-    // Display welcome message
-    CLIUtils.displaySection('BMAD™ Installation', 'Version ' + require(path.join(getProjectRoot(), 'package.json')).version);
+    // Check if core config was already collected in UI
+    const hasCoreConfig = config.coreConfig && Object.keys(config.coreConfig).length > 0;
 
-    // Preflight: Handle legacy BMAD v4 footprints before any prompts/writes
-    const projectDir = path.resolve(config.directory);
-    const legacyV4 = await this.detector.detectLegacyV4(projectDir);
-    if (legacyV4.hasLegacyV4) {
-      await this.handleLegacyV4Migration(projectDir, legacyV4);
+    // Only display logo if core config wasn't already collected (meaning we're not continuing from UI)
+    if (!hasCoreConfig) {
+      // Display BMAD logo
+      CLIUtils.displayLogo();
+
+      // Display welcome message
+      CLIUtils.displaySection('BMad™  Installation', 'Version ' + require(path.join(getProjectRoot(), 'package.json')).version);
     }
 
+    // Note: Legacy V4 detection now happens earlier in UI.promptInstall()
+    // before any config collection, so we don't need to check again here
+
+    const projectDir = path.resolve(config.directory);
+
     // If core config was pre-collected (from interactive mode), use it
-    if (config.coreConfig) {
+    if (config.coreConfig && Object.keys(config.coreConfig).length > 0) {
       this.configCollector.collectedConfig.core = config.coreConfig;
       // Also store in allAnswers for cross-referencing
       this.configCollector.allAnswers = {};
@@ -189,14 +400,125 @@ class Installer {
 
     // Collect configurations for modules (skip if quick update already collected them)
     let moduleConfigs;
+    let customModulePaths = new Map();
+
     if (config._quickUpdate) {
       // Quick update already collected all configs, use them directly
       moduleConfigs = this.configCollector.collectedConfig;
+
+      // For quick update, populate customModulePaths from _customModuleSources
+      if (config._customModuleSources) {
+        for (const [moduleId, customInfo] of config._customModuleSources) {
+          customModulePaths.set(moduleId, customInfo.sourcePath);
+        }
+      }
     } else {
-      // Regular install - collect configurations (core was already collected in UI.promptInstall if interactive)
-      moduleConfigs = await this.configCollector.collectAllConfigurations(config.modules || [], path.resolve(config.directory));
+      // For regular updates (modify flow), check manifest for custom module sources
+      if (config._isUpdate && config._existingInstall && config._existingInstall.customModules) {
+        for (const customModule of config._existingInstall.customModules) {
+          // Ensure we have an absolute sourcePath
+          let absoluteSourcePath = customModule.sourcePath;
+
+          // Check if sourcePath is a cache-relative path (starts with _config)
+          if (absoluteSourcePath && absoluteSourcePath.startsWith('_config')) {
+            // Convert cache-relative path to absolute path
+            absoluteSourcePath = path.join(bmadDir, absoluteSourcePath);
+          }
+          // If no sourcePath but we have relativePath, convert it
+          else if (!absoluteSourcePath && customModule.relativePath) {
+            // relativePath is relative to the project root (parent of bmad dir)
+            absoluteSourcePath = path.resolve(projectDir, customModule.relativePath);
+          }
+          // Ensure sourcePath is absolute for anything else
+          else if (absoluteSourcePath && !path.isAbsolute(absoluteSourcePath)) {
+            absoluteSourcePath = path.resolve(absoluteSourcePath);
+          }
+
+          if (absoluteSourcePath) {
+            customModulePaths.set(customModule.id, absoluteSourcePath);
+          }
+        }
+      }
+
+      // Build custom module paths map from customContent
+
+      // Handle selectedFiles (from existing install path or manual directory input)
+      if (config.customContent && config.customContent.selected && config.customContent.selectedFiles) {
+        const customHandler = new CustomHandler();
+        for (const customFile of config.customContent.selectedFiles) {
+          const customInfo = await customHandler.getCustomInfo(customFile, path.resolve(config.directory));
+          if (customInfo && customInfo.id) {
+            customModulePaths.set(customInfo.id, customInfo.path);
+          }
+        }
+      }
+
+      // Handle new custom content sources from UI
+      if (config.customContent && config.customContent.sources) {
+        for (const source of config.customContent.sources) {
+          customModulePaths.set(source.id, source.path);
+        }
+      }
+
+      // Handle cachedModules (from new install path where modules are cached)
+      // Only include modules that were actually selected for installation
+      if (config.customContent && config.customContent.cachedModules) {
+        // Get selected cached module IDs (if available)
+        const selectedCachedIds = config.customContent.selectedCachedModules || [];
+        // If no selection info, include all cached modules (for backward compatibility)
+        const shouldIncludeAll = selectedCachedIds.length === 0 && config.customContent.selected;
+
+        for (const cachedModule of config.customContent.cachedModules) {
+          // For cached modules, the path is the cachePath which contains the module.yaml
+          if (
+            cachedModule.id &&
+            cachedModule.cachePath && // Include if selected or if we should include all
+            (shouldIncludeAll || selectedCachedIds.includes(cachedModule.id))
+          ) {
+            customModulePaths.set(cachedModule.id, cachedModule.cachePath);
+          }
+        }
+      }
+
+      // Get list of all modules including custom modules
+      // Order: core first, then official modules, then custom modules
+      const allModulesForConfig = ['core'];
+
+      // Add official modules (excluding core and any custom modules)
+      const officialModules = (config.modules || []).filter((m) => m !== 'core' && !customModulePaths.has(m));
+      allModulesForConfig.push(...officialModules);
+
+      // Add custom modules at the end
+      for (const [moduleId] of customModulePaths) {
+        if (!allModulesForConfig.includes(moduleId)) {
+          allModulesForConfig.push(moduleId);
+        }
+      }
+
+      // Check if core was already collected in UI
+      if (config.coreConfig && Object.keys(config.coreConfig).length > 0) {
+        // Core already collected, skip it in config collection
+        const modulesWithoutCore = allModulesForConfig.filter((m) => m !== 'core');
+        moduleConfigs = await this.configCollector.collectAllConfigurations(modulesWithoutCore, path.resolve(config.directory), {
+          customModulePaths,
+        });
+      } else {
+        // Core not collected yet, include it
+        moduleConfigs = await this.configCollector.collectAllConfigurations(allModulesForConfig, path.resolve(config.directory), {
+          customModulePaths,
+        });
+      }
     }
 
+    // Store AgentVibes configuration for injection point processing
+    this.enableAgentVibes = config.enableAgentVibes || false;
+
+    // Set bmad folder name on module manager and IDE manager for placeholder replacement
+    this.moduleManager.setBmadFolderName(BMAD_FOLDER_NAME);
+    this.moduleManager.setCoreConfig(moduleConfigs.core || {});
+    this.moduleManager.setCustomModulePaths(customModulePaths);
+    this.ideManager.setBmadFolderName(BMAD_FOLDER_NAME);
+
     // Tool selection will be collected after we determine if it's a reinstall/update/new install
 
     const spinner = ora('Preparing installation...').start();
@@ -205,6 +527,9 @@ class Installer {
       // Resolve target directory (path.resolve handles platform differences)
       const projectDir = path.resolve(config.directory);
 
+      // Always use the standard _bmad folder name
+      const bmadDir = path.join(projectDir, BMAD_FOLDER_NAME);
+
       // Create a project directory if it doesn't exist (user already confirmed)
       if (!(await fs.pathExists(projectDir))) {
         spinner.text = 'Creating installation directory...';
@@ -225,8 +550,6 @@ class Installer {
         }
       }
 
-      const bmadDir = path.join(projectDir, 'bmad');
-
       // Check existing installation
       spinner.text = 'Checking for existing installation...';
       const existingInstall = await this.detector.detect(bmadDir);
@@ -236,9 +559,7 @@ class Installer {
 
         // Check if user already decided what to do (from early menu in ui.js)
         let action = null;
-        if (config._requestedReinstall) {
-          action = 'reinstall';
-        } else if (config.actionType === 'update') {
+        if (config.actionType === 'update') {
           action = 'update';
         } else {
           // Fallback: Ask the user (backwards compatibility for other code paths)
@@ -250,64 +571,49 @@ class Installer {
           action = promptResult.action;
         }
 
-        if (action === 'cancel') {
-          console.log('Installation cancelled.');
-          return { success: false, cancelled: true };
-        }
-
-        if (action === 'reinstall') {
-          // Warn about destructive operation
-          console.log(chalk.red.bold('\n⚠️  WARNING: This is a destructive operation!'));
-          console.log(chalk.red('All custom files and modifications in the bmad directory will be lost.'));
-
-          const inquirer = require('inquirer');
-          const { confirmReinstall } = await inquirer.prompt([
-            {
-              type: 'confirm',
-              name: 'confirmReinstall',
-              message: chalk.yellow('Are you sure you want to delete and reinstall?'),
-              default: false,
-            },
-          ]);
-
-          if (!confirmReinstall) {
-            console.log('Installation cancelled.');
-            return { success: false, cancelled: true };
-          }
-
-          // Remember previously configured IDEs before deleting
-          config._previouslyConfiguredIdes = existingInstall.ides || [];
-
-          // Remove existing installation
-          await fs.remove(bmadDir);
-          console.log(chalk.green('✓ Removed existing installation\n'));
-
-          // Mark this as a full reinstall so we re-collect IDE configurations
-          config._isFullReinstall = true;
-        } else if (action === 'update') {
+        if (action === 'update') {
           // Store that we're updating for later processing
           config._isUpdate = true;
           config._existingInstall = existingInstall;
 
           // Detect custom and modified files BEFORE updating (compare current files vs files-manifest.csv)
           const existingFilesManifest = await this.readFilesManifest(bmadDir);
-          console.log(chalk.dim(`DEBUG: Read ${existingFilesManifest.length} files from manifest`));
-          console.log(chalk.dim(`DEBUG: Manifest has hashes: ${existingFilesManifest.some((f) => f.hash)}`));
-
           const { customFiles, modifiedFiles } = await this.detectCustomFiles(bmadDir, existingFilesManifest);
 
-          console.log(chalk.dim(`DEBUG: Found ${customFiles.length} custom files, ${modifiedFiles.length} modified files`));
-          if (modifiedFiles.length > 0) {
-            console.log(chalk.yellow('DEBUG: Modified files:'));
-            for (const f of modifiedFiles) console.log(chalk.dim(`  - ${f.path}`));
-          }
-
           config._customFiles = customFiles;
           config._modifiedFiles = modifiedFiles;
 
+          // Also check cache directory for custom modules (like quick update does)
+          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;
+
+                // Skip if we already have this module from manifest
+                if (customModulePaths.has(moduleId)) {
+                  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);
+          }
+
           // If there are custom files, back them up temporarily
           if (customFiles.length > 0) {
-            const tempBackupDir = path.join(projectDir, '.bmad-custom-backup-temp');
+            const tempBackupDir = path.join(projectDir, '_bmad-custom-backup-temp');
             await fs.ensureDir(tempBackupDir);
 
             spinner.start(`Backing up ${customFiles.length} custom files...`);
@@ -324,23 +630,19 @@ class Installer {
 
           // For modified files, back them up to temp directory (will be restored as .bak files after install)
           if (modifiedFiles.length > 0) {
-            const tempModifiedBackupDir = path.join(projectDir, '.bmad-modified-backup-temp');
+            const tempModifiedBackupDir = path.join(projectDir, '_bmad-modified-backup-temp');
             await fs.ensureDir(tempModifiedBackupDir);
 
-            console.log(chalk.yellow(`\nDEBUG: Backing up ${modifiedFiles.length} modified files to temp location`));
             spinner.start(`Backing up ${modifiedFiles.length} modified files...`);
             for (const modifiedFile of modifiedFiles) {
               const relativePath = path.relative(bmadDir, modifiedFile.path);
               const tempBackupPath = path.join(tempModifiedBackupDir, relativePath);
-              console.log(chalk.dim(`DEBUG: Backing up ${relativePath} to temp`));
               await fs.ensureDir(path.dirname(tempBackupPath));
               await fs.copy(modifiedFile.path, tempBackupPath, { overwrite: true });
             }
             spinner.succeed(`Backed up ${modifiedFiles.length} modified files`);
 
             config._tempModifiedBackupDir = tempModifiedBackupDir;
-          } else {
-            console.log(chalk.dim('DEBUG: No modified files detected'));
           }
         }
       } else if (existingInstall.installed && config._quickUpdate) {
@@ -356,9 +658,37 @@ class Installer {
         config._customFiles = customFiles;
         config._modifiedFiles = modifiedFiles;
 
+        // Also check cache directory for custom modules (like quick update does)
+        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;
+
+              // Skip if we already have this module from manifest
+              if (customModulePaths.has(moduleId)) {
+                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);
+        }
+
         // Back up custom files
         if (customFiles.length > 0) {
-          const tempBackupDir = path.join(projectDir, '.bmad-custom-backup-temp');
+          const tempBackupDir = path.join(projectDir, '_bmad-custom-backup-temp');
           await fs.ensureDir(tempBackupDir);
 
           spinner.start(`Backing up ${customFiles.length} custom files...`);
@@ -374,7 +704,7 @@ class Installer {
 
         // Back up modified files
         if (modifiedFiles.length > 0) {
-          const tempModifiedBackupDir = path.join(projectDir, '.bmad-modified-backup-temp');
+          const tempModifiedBackupDir = path.join(projectDir, '_bmad-modified-backup-temp');
           await fs.ensureDir(tempModifiedBackupDir);
 
           spinner.start(`Backing up ${modifiedFiles.length} modified files...`);
@@ -429,44 +759,229 @@ class Installer {
       config.skipIde = toolSelection.skipIde;
       const ideConfigurations = toolSelection.configurations;
 
-      spinner.start('Continuing installation...');
+      if (spinner.isSpinning) {
+        spinner.text = 'Continuing installation...';
+      } else {
+        spinner.start('Continuing installation...');
+      }
 
       // Create bmad directory structure
       spinner.text = 'Creating directory structure...';
       await this.createDirectoryStructure(bmadDir);
 
-      // Resolve dependencies for selected modules
-      spinner.text = 'Resolving dependencies...';
-      const projectRoot = getProjectRoot();
-      const modulesToInstall = config.installCore ? ['core', ...config.modules] : config.modules;
+      // Cache custom modules if any
+      if (customModulePaths && customModulePaths.size > 0) {
+        spinner.text = 'Caching custom modules...';
+        const { CustomModuleCache } = require('./custom-module-cache');
+        const customCache = new CustomModuleCache(bmadDir);
 
-      // For dependency resolution, we need to pass the project root
-      const resolution = await this.dependencyResolver.resolve(projectRoot, config.modules || [], { verbose: config.verbose });
+        for (const [moduleId, sourcePath] of customModulePaths) {
+          const cachedInfo = await customCache.cacheModule(moduleId, sourcePath, {
+            sourcePath: sourcePath, // Store original path for updates
+          });
 
-      if (config.verbose) {
-        spinner.succeed('Dependencies resolved');
-      } else {
-        spinner.succeed('Dependencies resolved');
+          // Update the customModulePaths to use the cached location
+          customModulePaths.set(moduleId, cachedInfo.cachePath);
+        }
+
+        // Update module manager with the cached paths
+        this.moduleManager.setCustomModulePaths(customModulePaths);
+        spinner.succeed('Custom modules cached');
       }
 
-      // Install core if requested or if dependencies require it
-      if (config.installCore || resolution.byModule.core) {
+      const projectRoot = getProjectRoot();
+
+      // Step 1: Install core module first (if requested)
+      if (config.installCore) {
         spinner.start('Installing BMAD core...');
-        await this.installCoreWithDependencies(bmadDir, resolution.byModule.core);
+        await this.installCoreWithDependencies(bmadDir, { core: {} });
         spinner.succeed('Core installed');
+
+        // Generate core config file
+        await this.generateModuleConfigs(bmadDir, { core: config.coreConfig || {} });
+      }
+
+      // Custom content is already handled in UI before module selection
+      let finalCustomContent = config.customContent;
+
+      // Step 3: Prepare modules list including cached custom modules
+      let allModules = [...(config.modules || [])];
+
+      // During quick update, we might have custom module sources from the manifest
+      if (config._customModuleSources) {
+        // Add custom modules from stored sources
+        for (const [moduleId, customInfo] of config._customModuleSources) {
+          if (!allModules.includes(moduleId) && (await fs.pathExists(customInfo.sourcePath))) {
+            allModules.push(moduleId);
+          }
+        }
+      }
+
+      // Add cached custom modules
+      if (finalCustomContent && finalCustomContent.cachedModules) {
+        for (const cachedModule of finalCustomContent.cachedModules) {
+          if (!allModules.includes(cachedModule.id)) {
+            allModules.push(cachedModule.id);
+          }
+        }
+      }
+
+      // Regular custom content from user input (non-cached)
+      if (finalCustomContent && finalCustomContent.selected && finalCustomContent.selectedFiles) {
+        // Add custom modules to the installation list
+        const customHandler = new CustomHandler();
+        for (const customFile of finalCustomContent.selectedFiles) {
+          const customInfo = await customHandler.getCustomInfo(customFile, projectDir);
+          if (customInfo && customInfo.id) {
+            allModules.push(customInfo.id);
+          }
+        }
+      }
+
+      // Don't include core again if already installed
+      if (config.installCore) {
+        allModules = allModules.filter((m) => m !== 'core');
       }
 
+      const modulesToInstall = allModules;
+
+      // For dependency resolution, we only need regular modules (not custom modules)
+      // Custom modules are already installed in _bmad and don't need dependency resolution from source
+      const regularModulesForResolution = allModules.filter((module) => {
+        // Check if this is a custom module
+        const isCustom =
+          customModulePaths.has(module) ||
+          (finalCustomContent && finalCustomContent.cachedModules && finalCustomContent.cachedModules.some((cm) => cm.id === module)) ||
+          (finalCustomContent &&
+            finalCustomContent.selected &&
+            finalCustomContent.selectedFiles &&
+            finalCustomContent.selectedFiles.some((f) => f.includes(module)));
+        return !isCustom;
+      });
+
+      // For dependency resolution, we need to pass the project root
+      // Create a temporary module manager that knows about custom content locations
+      const tempModuleManager = new ModuleManager({
+        bmadDir: bmadDir, // Pass bmadDir so we can check cache
+      });
+
+      const resolution = await this.dependencyResolver.resolve(projectRoot, regularModulesForResolution, {
+        verbose: config.verbose,
+        moduleManager: tempModuleManager,
+      });
+
+      spinner.succeed('Dependencies resolved');
+
       // Install modules with their dependencies
-      if (config.modules && config.modules.length > 0) {
-        for (const moduleName of config.modules) {
-          spinner.start(`Installing module: ${moduleName}...`);
-          await this.installModuleWithDependencies(moduleName, bmadDir, resolution.byModule[moduleName]);
-          spinner.succeed(`Module installed: ${moduleName}`);
+      if (allModules && allModules.length > 0) {
+        const installedModuleNames = new Set();
+
+        for (const moduleName of allModules) {
+          // Skip if already installed
+          if (installedModuleNames.has(moduleName)) {
+            continue;
+          }
+          installedModuleNames.add(moduleName);
+
+          // Show appropriate message based on whether this is a quick update
+          const isQuickUpdate = config._quickUpdate || false;
+          spinner.start(`${isQuickUpdate ? 'Updating' : 'Installing'} module: ${moduleName}...`);
+
+          // Check if this is a custom module
+          let isCustomModule = false;
+          let customInfo = null;
+          let useCache = false;
+
+          // First check if we have a cached version
+          if (finalCustomContent && finalCustomContent.cachedModules) {
+            const cachedModule = finalCustomContent.cachedModules.find((m) => m.id === moduleName);
+            if (cachedModule) {
+              isCustomModule = true;
+              customInfo = {
+                id: moduleName,
+                path: cachedModule.cachePath,
+                config: {},
+              };
+              useCache = true;
+            }
+          }
+
+          // Then check if we have custom module sources from the manifest (for quick update)
+          if (!isCustomModule && config._customModuleSources && config._customModuleSources.has(moduleName)) {
+            customInfo = config._customModuleSources.get(moduleName);
+            isCustomModule = true;
+
+            // Check if this is a cached module (source path starts with _config)
+            if (
+              customInfo.sourcePath &&
+              (customInfo.sourcePath.startsWith('_config') || customInfo.sourcePath.includes('_config/custom'))
+            ) {
+              useCache = true;
+              // Make sure we have the right path structure
+              if (!customInfo.path) {
+                customInfo.path = customInfo.sourcePath;
+              }
+            }
+          }
+
+          // Finally check regular custom content
+          if (!isCustomModule && finalCustomContent && finalCustomContent.selected && finalCustomContent.selectedFiles) {
+            const customHandler = new CustomHandler();
+            for (const customFile of finalCustomContent.selectedFiles) {
+              const info = await customHandler.getCustomInfo(customFile, projectDir);
+              if (info && info.id === moduleName) {
+                isCustomModule = true;
+                customInfo = info;
+                break;
+              }
+            }
+          }
+
+          if (isCustomModule && customInfo) {
+            // Custom modules are now installed via ModuleManager just like standard modules
+            // The custom module path should already be in customModulePaths from earlier setup
+            if (!customModulePaths.has(moduleName) && customInfo.path) {
+              customModulePaths.set(moduleName, customInfo.path);
+              this.moduleManager.setCustomModulePaths(customModulePaths);
+            }
+
+            const collectedModuleConfig = moduleConfigs[moduleName] || {};
+
+            // Use ModuleManager to install the custom module
+            await this.moduleManager.install(
+              moduleName,
+              bmadDir,
+              (filePath) => {
+                this.installedFiles.add(filePath);
+              },
+              {
+                isCustom: true,
+                moduleConfig: collectedModuleConfig,
+                isQuickUpdate: config._quickUpdate || false,
+                installer: this,
+              },
+            );
+
+            // Create module config (include collected config from module.yaml prompts)
+            await this.generateModuleConfigs(bmadDir, {
+              [moduleName]: { ...config.coreConfig, ...customInfo.config, ...collectedModuleConfig },
+            });
+          } else {
+            // Regular module installation
+            // Special case for core module
+            if (moduleName === 'core') {
+              await this.installCoreWithDependencies(bmadDir, resolution.byModule[moduleName]);
+            } else {
+              await this.installModuleWithDependencies(moduleName, bmadDir, resolution.byModule[moduleName]);
+            }
+          }
+
+          spinner.succeed(`Module ${isQuickUpdate ? 'updated' : 'installed'}: ${moduleName}`);
         }
 
         // Install partial modules (only dependencies)
         for (const [module, files] of Object.entries(resolution.byModule)) {
-          if (!config.modules.includes(module) && module !== 'core') {
+          if (!allModules.includes(module) && module !== 'core') {
             const totalFiles =
               files.agents.length +
               files.tasks.length +
@@ -483,6 +998,8 @@ class Installer {
         }
       }
 
+      // All content is now installed as modules - no separate custom content handling needed
+
       // Generate clean config.yaml files for each installed module
       spinner.start('Generating module configurations...');
       await this.generateModuleConfigs(bmadDir, moduleConfigs);
@@ -493,26 +1010,41 @@ class Installer {
       // Customize templates are now created in processAgentFiles when building YAML agents
 
       // Pre-register manifest files that will be created (except files-manifest.csv to avoid recursion)
-      const cfgDir = path.join(bmadDir, '_cfg');
-      this.installedFiles.push(
-        path.join(cfgDir, 'manifest.yaml'),
-        path.join(cfgDir, 'workflow-manifest.csv'),
-        path.join(cfgDir, 'agent-manifest.csv'),
-        path.join(cfgDir, 'task-manifest.csv'),
-      );
+      const cfgDir = path.join(bmadDir, '_config');
+      this.installedFiles.add(path.join(cfgDir, 'manifest.yaml'));
+      this.installedFiles.add(path.join(cfgDir, 'workflow-manifest.csv'));
+      this.installedFiles.add(path.join(cfgDir, 'agent-manifest.csv'));
+      this.installedFiles.add(path.join(cfgDir, 'task-manifest.csv'));
 
       // Generate CSV manifests for workflows, agents, tasks AND ALL FILES with hashes BEFORE IDE setup
       spinner.start('Generating workflow and agent manifests...');
       const manifestGen = new ManifestGenerator();
 
-      // Include preserved modules (from quick update) in the manifest
-      const allModulesToList = config._preserveModules ? [...(config.modules || []), ...config._preserveModules] : config.modules || [];
+      // For quick update, we need ALL installed modules in the manifest
+      // Not just the ones being updated
+      const allModulesForManifest = config._quickUpdate
+        ? config._existingModules || allModules || []
+        : config._preserveModules
+          ? [...allModules, ...config._preserveModules]
+          : allModules || [];
+
+      // For regular installs (including when called from quick update), use what we have
+      let modulesForCsvPreserve;
+      if (config._quickUpdate) {
+        // Quick update - use existing modules or fall back to modules being updated
+        modulesForCsvPreserve = config._existingModules || allModules || [];
+      } else {
+        // Regular install - use the modules we're installing plus any preserved ones
+        modulesForCsvPreserve = config._preserveModules ? [...allModules, ...config._preserveModules] : allModules;
+      }
 
-      const manifestStats = await manifestGen.generateManifests(bmadDir, config.modules || [], this.installedFiles, {
+      const manifestStats = await manifestGen.generateManifests(bmadDir, allModulesForManifest, [...this.installedFiles], {
         ides: config.ides || [],
-        preservedModules: config._preserveModules || [], // Scan these from installed bmad/ dir
+        preservedModules: modulesForCsvPreserve, // Scan these from installed bmad/ dir
       });
 
+      // Custom modules are now included in the main modules list - no separate tracking needed
+
       spinner.succeed(
         `Manifests generated: ${manifestStats.workflows} workflows, ${manifestStats.agents} agents, ${manifestStats.tasks} tasks, ${manifestStats.tools} tools, ${manifestStats.files} files`,
       );
@@ -552,7 +1084,7 @@ class Installer {
 
             // Pass pre-collected configuration to avoid re-prompting
             await this.ideManager.setup(ide, projectDir, bmadDir, {
-              selectedModules: config.modules || [],
+              selectedModules: allModules || [],
               preCollectedConfig: ideConfigurations[ide] || null,
               verbose: config.verbose,
             });
@@ -572,24 +1104,24 @@ class Installer {
           console.log = originalLog;
 
           if (spinner.isSpinning) {
-            spinner.succeed(`Configured ${validIdes.length} IDE${validIdes.length > 1 ? 's' : ''}`);
+            spinner.succeed(`Configured: ${validIdes.join(', ')}`);
           } else {
-            console.log(chalk.green(`✓ Configured ${validIdes.length} IDE${validIdes.length > 1 ? 's' : ''}`));
+            console.log(chalk.green(`✓ Configured: ${validIdes.join(', ')}`));
           }
         }
-
-        // Copy IDE-specific documentation (only for valid IDEs)
-        const validIdesForDocs = (config.ides || []).filter((ide) => ide && typeof ide === 'string');
-        if (validIdesForDocs.length > 0) {
-          spinner.start('Copying IDE documentation...');
-          await this.copyIdeDocumentation(validIdesForDocs, bmadDir);
-          spinner.succeed('IDE documentation copied');
-        }
       }
 
       // Run module-specific installers after IDE setup
       spinner.start('Running module-specific installers...');
 
+      // Create a conditional logger based on verbose mode
+      const verboseMode = process.env.BMAD_VERBOSE_INSTALL === 'true' || config.verbose;
+      const moduleLogger = {
+        log: (msg) => (verboseMode ? console.log(msg) : {}), // Only log in verbose mode
+        error: (msg) => console.error(msg), // Always show errors
+        warn: (msg) => console.warn(msg), // Always show warnings
+      };
+
       // Run core module installer if core was installed
       if (config.installCore || resolution.byModule.core) {
         spinner.text = 'Running core module installer...';
@@ -597,11 +1129,8 @@ class Installer {
         await this.moduleManager.runModuleInstaller('core', bmadDir, {
           installedIDEs: config.ides || [],
           moduleConfig: moduleConfigs.core || {},
-          logger: {
-            log: (msg) => console.log(msg),
-            error: (msg) => console.error(msg),
-            warn: (msg) => console.warn(msg),
-          },
+          coreConfig: moduleConfigs.core || {},
+          logger: moduleLogger,
         });
       }
 
@@ -614,11 +1143,8 @@ class Installer {
           await this.moduleManager.runModuleInstaller(moduleName, bmadDir, {
             installedIDEs: config.ides || [],
             moduleConfig: moduleConfigs[moduleName] || {},
-            logger: {
-              log: (msg) => console.log(msg),
-              error: (msg) => console.error(msg),
-              warn: (msg) => console.warn(msg),
-            },
+            coreConfig: moduleConfigs.core || {},
+            logger: moduleLogger,
           });
         }
       }
@@ -685,21 +1211,16 @@ class Installer {
       // Report custom and modified files if any were found
       if (customFiles.length > 0) {
         console.log(chalk.cyan(`\n📁 Custom files preserved: ${customFiles.length}`));
-        console.log(chalk.dim('The following custom files were found and restored:\n'));
-        for (const file of customFiles) {
-          console.log(chalk.dim(`  - ${path.relative(bmadDir, file)}`));
-        }
-        console.log('');
       }
 
       if (modifiedFiles.length > 0) {
-        console.log(chalk.yellow(`\n⚠️  Modified files detected: ${modifiedFiles.length}`));
-        console.log(chalk.dim('The following files were modified and backed up with .bak extension:\n'));
-        for (const file of modifiedFiles) {
-          console.log(chalk.dim(`  - ${file.relativePath} → ${file.relativePath}.bak`));
-        }
-        console.log(chalk.dim('\nThese files have been updated with the new version.'));
-        console.log(chalk.dim('Review the .bak files to see your changes and merge if needed.\n'));
+        console.log(chalk.yellow(`\n⚠️  User modified files detected: ${modifiedFiles.length}`));
+        console.log(
+          chalk.dim(
+            '\nThese user modified files have been updated with the new version, search the project for .bak files that had your customizations.',
+          ),
+        );
+        console.log(chalk.dim('Remove these .bak files it no longer needed\n'));
       }
 
       // Display completion message
@@ -710,9 +1231,18 @@ class Installer {
         modules: config.modules,
         ides: config.ides,
         customFiles: customFiles.length > 0 ? customFiles : undefined,
+        ttsInjectedFiles: this.enableAgentVibes && this.ttsInjectedFiles.length > 0 ? this.ttsInjectedFiles : undefined,
+        agentVibesEnabled: this.enableAgentVibes || false,
       });
 
-      return { success: true, path: bmadDir, modules: config.modules, ides: config.ides };
+      return {
+        success: true,
+        path: bmadDir,
+        modules: config.modules,
+        ides: config.ides,
+        needsAgentVibes: this.enableAgentVibes && !config.agentVibesInstalled,
+        projectDir: projectDir,
+      };
     } catch (error) {
       spinner.fail('Installation failed');
       throw error;
@@ -726,7 +1256,8 @@ class Installer {
     const spinner = ora('Checking installation...').start();
 
     try {
-      const bmadDir = path.join(path.resolve(config.directory), 'bmad');
+      const projectDir = path.resolve(config.directory);
+      const { bmadDir } = await this.findBmadDir(projectDir);
       const existingInstall = await this.detector.detect(bmadDir);
 
       if (!existingInstall.installed) {
@@ -740,6 +1271,62 @@ class Installer {
       const currentVersion = existingInstall.version;
       const newVersion = require(path.join(getProjectRoot(), 'package.json')).version;
 
+      // Check for custom modules with missing sources before update
+      const customModuleSources = new Map();
+
+      // Check manifest for backward compatibility
+      if (existingInstall.customModules) {
+        for (const customModule of existingInstall.customModules) {
+          customModuleSources.set(customModule.id, customModule);
+        }
+      }
+
+      // Also check cache directory
+      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;
+
+            // Skip if we already have this module
+            if (customModuleSources.has(moduleId)) {
+              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)) {
+              customModuleSources.set(moduleId, {
+                id: moduleId,
+                name: moduleId,
+                sourcePath: path.join('_config', 'custom', moduleId), // Relative path
+                cached: true,
+              });
+            }
+          }
+        }
+      }
+
+      if (customModuleSources.size > 0) {
+        spinner.stop();
+        console.log(chalk.yellow('\nChecking custom module sources before update...'));
+
+        const projectRoot = getProjectRoot();
+        await this.handleMissingCustomSources(
+          customModuleSources,
+          bmadDir,
+          projectRoot,
+          'update',
+          existingInstall.modules.map((m) => m.id),
+        );
+
+        spinner.start('Preparing update...');
+      }
+
       if (config.dryRun) {
         spinner.stop();
         console.log(chalk.cyan('\n🔍 Update Preview (Dry Run)\n'));
@@ -786,7 +1373,8 @@ class Installer {
    * Get installation status
    */
   async getStatus(directory) {
-    const bmadDir = path.join(path.resolve(directory), 'bmad');
+    const projectDir = path.resolve(directory);
+    const { bmadDir } = await this.findBmadDir(projectDir);
     return await this.detector.detect(bmadDir);
   }
 
@@ -801,14 +1389,15 @@ class Installer {
    * Uninstall BMAD
    */
   async uninstall(directory) {
-    const bmadDir = path.join(path.resolve(directory), 'bmad');
+    const projectDir = path.resolve(directory);
+    const { bmadDir } = await this.findBmadDir(projectDir);
 
     if (await fs.pathExists(bmadDir)) {
       await fs.remove(bmadDir);
     }
 
     // Clean up IDE configurations
-    await this.ideManager.cleanup(path.resolve(directory));
+    await this.ideManager.cleanup(projectDir);
 
     return { success: true };
   }
@@ -818,8 +1407,9 @@ class Installer {
    */
   async createDirectoryStructure(bmadDir) {
     await fs.ensureDir(bmadDir);
-    await fs.ensureDir(path.join(bmadDir, '_cfg'));
-    await fs.ensureDir(path.join(bmadDir, '_cfg', 'agents'));
+    await fs.ensureDir(path.join(bmadDir, '_config'));
+    await fs.ensureDir(path.join(bmadDir, '_config', 'agents'));
+    await fs.ensureDir(path.join(bmadDir, '_config', 'custom'));
   }
 
   /**
@@ -828,7 +1418,7 @@ class Installer {
    * @param {Object} moduleConfigs - Collected configuration values
    */
   async generateModuleConfigs(bmadDir, moduleConfigs) {
-    const yaml = require('js-yaml');
+    const yaml = require('yaml');
 
     // Extract core config values to share with other modules
     const coreConfig = moduleConfigs.core || {};
@@ -836,7 +1426,7 @@ class Installer {
     // Get all installed module directories
     const entries = await fs.readdir(bmadDir, { withFileTypes: true });
     const installedModules = entries
-      .filter((entry) => entry.isDirectory() && entry.name !== '_cfg' && entry.name !== 'docs')
+      .filter((entry) => entry.isDirectory() && entry.name !== '_config' && entry.name !== 'docs')
       .map((entry) => entry.name);
 
     // Generate config.yaml for each installed module
@@ -874,12 +1464,14 @@ class Installer {
           coreSection = '\n# Core Configuration Values\n';
         }
 
+        // Clean the config to remove any non-serializable values (like functions)
+        const cleanConfig = structuredClone(finalConfig);
+
         // Convert config to YAML
-        let yamlContent = yaml.dump(finalConfig, {
+        let yamlContent = yaml.stringify(cleanConfig, {
           indent: 2,
-          lineWidth: -1,
-          noRefs: true,
-          sortKeys: false,
+          lineWidth: 0,
+          minContentWidth: 0,
         });
 
         // If we have core values, reorganize the YAML to group them with their comment
@@ -906,11 +1498,12 @@ class Installer {
           }
         }
 
-        // Write the clean config file
-        await fs.writeFile(configPath, header + yamlContent, 'utf8');
+        // Write the clean config file with POSIX-compliant final newline
+        const content = header + yamlContent;
+        await fs.writeFile(configPath, content.endsWith('\n') ? content : content + '\n', 'utf8');
 
         // Track the config file in installedFiles
-        this.installedFiles.push(configPath);
+        this.installedFiles.add(configPath);
       }
     }
   }
@@ -923,14 +1516,7 @@ class Installer {
   async installCoreWithDependencies(bmadDir, coreFiles) {
     const sourcePath = getModulePath('core');
     const targetPath = path.join(bmadDir, 'core');
-
-    // Install full core
     await this.installCore(bmadDir);
-
-    // If there are specific dependency files, ensure they're included
-    if (coreFiles) {
-      // Already handled by installCore for core module
-    }
   }
 
   /**
@@ -949,11 +1535,12 @@ class Installer {
       moduleName,
       bmadDir,
       (filePath) => {
-        this.installedFiles.push(filePath);
+        this.installedFiles.add(filePath);
       },
       {
         skipModuleInstaller: true, // We'll run it later after IDE setup
         moduleConfig: moduleConfig, // Pass module config for conditional filtering
+        installer: this,
       },
     );
 
@@ -985,8 +1572,8 @@ class Installer {
         const targetPath = path.join(agentsDir, fileName);
 
         if (await fs.pathExists(sourcePath)) {
-          await fs.copy(sourcePath, targetPath);
-          this.installedFiles.push(targetPath);
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
         }
       }
     }
@@ -1001,8 +1588,8 @@ class Installer {
         const targetPath = path.join(tasksDir, fileName);
 
         if (await fs.pathExists(sourcePath)) {
-          await fs.copy(sourcePath, targetPath);
-          this.installedFiles.push(targetPath);
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
         }
       }
     }
@@ -1017,8 +1604,8 @@ class Installer {
         const targetPath = path.join(toolsDir, fileName);
 
         if (await fs.pathExists(sourcePath)) {
-          await fs.copy(sourcePath, targetPath);
-          this.installedFiles.push(targetPath);
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
         }
       }
     }
@@ -1033,8 +1620,8 @@ class Installer {
         const targetPath = path.join(templatesDir, fileName);
 
         if (await fs.pathExists(sourcePath)) {
-          await fs.copy(sourcePath, targetPath);
-          this.installedFiles.push(targetPath);
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
         }
       }
     }
@@ -1048,8 +1635,8 @@ class Installer {
         await fs.ensureDir(path.dirname(targetPath));
 
         if (await fs.pathExists(dataPath)) {
-          await fs.copy(dataPath, targetPath);
-          this.installedFiles.push(targetPath);
+          await this.copyFileWithPlaceholderReplacement(dataPath, targetPath);
+          this.installedFiles.add(targetPath);
         }
       }
     }
@@ -1070,25 +1657,55 @@ class Installer {
     const sourcePath = getModulePath('core');
     const targetPath = path.join(bmadDir, 'core');
 
-    // Copy core files with filtering for localskip agents
-    await this.copyDirectoryWithFiltering(sourcePath, targetPath);
+    // Copy core files (skip .agent.yaml files like modules do)
+    await this.copyCoreFiles(sourcePath, targetPath);
+
+    // Compile agents using the same compiler as modules
+    const { ModuleManager } = require('../modules/manager');
+    const moduleManager = new ModuleManager();
+    await moduleManager.compileModuleAgents(sourcePath, targetPath, 'core', bmadDir, this);
 
     // Process agent files to inject activation block
     await this.processAgentFiles(targetPath, 'core');
   }
 
   /**
-   * Copy directory with filtering for localskip agents
-   * @param {string} sourcePath - Source directory path
-   * @param {string} targetPath - Target directory path
+   * Copy core files (similar to copyModuleWithFiltering but for core)
+   * @param {string} sourcePath - Source path
+   * @param {string} targetPath - Target path
    */
-  async copyDirectoryWithFiltering(sourcePath, targetPath) {
-    // Get all files in source directory
+  async copyCoreFiles(sourcePath, targetPath) {
+    // Get all files in source
     const files = await this.getFileList(sourcePath);
 
     for (const file of files) {
+      // Skip sub-modules directory - these are IDE-specific and handled separately
+      if (file.startsWith('sub-modules/')) {
+        continue;
+      }
+
+      // Skip sidecar directories - they are handled separately during agent compilation
+      if (
+        path
+          .dirname(file)
+          .split('/')
+          .some((dir) => dir.toLowerCase().includes('sidecar'))
+      ) {
+        continue;
+      }
+
+      // Skip _module-installer directory - it's only needed at install time
+      if (file.startsWith('_module-installer/') || file === 'module.yaml') {
+        continue;
+      }
+
       // Skip config.yaml templates - we'll generate clean ones with actual values
-      if (file === 'config.yaml' || file.endsWith('/config.yaml')) {
+      if (file === 'config.yaml' || file.endsWith('/config.yaml') || file === 'custom.yaml' || file.endsWith('/custom.yaml')) {
+        continue;
+      }
+
+      // Skip .agent.yaml files - they will be compiled separately
+      if (file.endsWith('.agent.yaml')) {
         continue;
       }
 
@@ -1096,7 +1713,7 @@ class Installer {
       const targetFile = path.join(targetPath, file);
 
       // Check if this is an agent file
-      if (file.includes('agents/') && file.endsWith('.md')) {
+      if (file.startsWith('agents/') && file.endsWith('.md')) {
         // Read the file to check for localskip
         const content = await fs.readFile(sourceFile, 'utf8');
 
@@ -1108,12 +1725,12 @@ class Installer {
         }
       }
 
-      // Copy the file
+      // Copy the file with placeholder replacement
       await fs.ensureDir(path.dirname(targetFile));
-      await fs.copy(sourceFile, targetFile, { overwrite: true });
+      await this.copyFileWithPlaceholderReplacement(sourceFile, targetFile);
 
       // Track the installed file
-      this.installedFiles.push(targetFile);
+      this.installedFiles.add(targetFile);
     }
   }
 
@@ -1160,363 +1777,45 @@ class Installer {
 
     // Determine project directory (parent of bmad/ directory)
     const bmadDir = path.dirname(modulePath);
-    const projectDir = path.dirname(bmadDir);
-    const cfgAgentsDir = path.join(bmadDir, '_cfg', 'agents');
+    const cfgAgentsDir = path.join(bmadDir, '_config', 'agents');
 
-    // Ensure _cfg/agents directory exists
+    // Ensure _config/agents directory exists
     await fs.ensureDir(cfgAgentsDir);
 
     // Get all agent files
     const agentFiles = await fs.readdir(agentsPath);
 
     for (const agentFile of agentFiles) {
-      // Handle YAML agents - build them to .md
+      // Skip .agent.yaml files - they should already be compiled by compileModuleAgents
       if (agentFile.endsWith('.agent.yaml')) {
-        const agentName = agentFile.replace('.agent.yaml', '');
-        const yamlPath = path.join(agentsPath, agentFile);
-        const mdPath = path.join(agentsPath, `${agentName}.md`);
-        const customizePath = path.join(cfgAgentsDir, `${moduleName}-${agentName}.customize.yaml`);
-
-        // Create customize template if it doesn't exist
-        if (!(await fs.pathExists(customizePath))) {
-          const genericTemplatePath = getSourcePath('utility', 'templates', 'agent.customize.template.yaml');
-          if (await fs.pathExists(genericTemplatePath)) {
-            await fs.copy(genericTemplatePath, customizePath);
-            console.log(chalk.dim(`  Created customize: ${moduleName}-${agentName}.customize.yaml`));
-          }
-        }
-
-        // Build YAML + customize to .md
-        const customizeExists = await fs.pathExists(customizePath);
-        const xmlContent = await this.xmlHandler.buildFromYaml(yamlPath, customizeExists ? customizePath : null, {
-          includeMetadata: true,
-        });
-
-        // DO NOT replace {project-root} - LLMs understand this placeholder at runtime
-        // const processedContent = xmlContent.replaceAll('{project-root}', projectDir);
-
-        // Write the built .md file to bmad/{module}/agents/
-        await fs.writeFile(mdPath, xmlContent, 'utf8');
-        this.installedFiles.push(mdPath);
-
-        // Remove the source YAML file - we can regenerate from installer source if needed
-        await fs.remove(yamlPath);
+        continue;
+      }
 
-        console.log(chalk.dim(`  Built agent: ${agentName}.md`));
+      // Only process .md files (already compiled from YAML)
+      if (!agentFile.endsWith('.md')) {
+        continue;
       }
-      // Handle legacy .md agents - inject activation if needed
-      else if (agentFile.endsWith('.md')) {
-        const agentPath = path.join(agentsPath, agentFile);
-        let content = await fs.readFile(agentPath, 'utf8');
 
-        // Check if content has agent XML and no activation block
-        if (content.includes('<agent') && !content.includes('<activation')) {
-          // Inject the activation block using XML handler
-          content = this.xmlHandler.injectActivationSimple(content);
-          await fs.writeFile(agentPath, content, 'utf8');
+      const agentName = agentFile.replace('.md', '');
+      const mdPath = path.join(agentsPath, agentFile);
+      const customizePath = path.join(cfgAgentsDir, `${moduleName}-${agentName}.customize.yaml`);
+
+      // For .md files that are already compiled, we don't need to do much
+      // Just ensure the customize template exists
+      if (!(await fs.pathExists(customizePath))) {
+        const genericTemplatePath = getSourcePath('utility', 'agent-components', 'agent.customize.template.yaml');
+        if (await fs.pathExists(genericTemplatePath)) {
+          await this.copyFileWithPlaceholderReplacement(genericTemplatePath, customizePath);
+          if (process.env.BMAD_VERBOSE_INSTALL === 'true') {
+            console.log(chalk.dim(`  Created customize: ${moduleName}-${agentName}.customize.yaml`));
+          }
         }
       }
     }
   }
 
   /**
-   * Build standalone agents in bmad/agents/ directory
-   * @param {string} bmadDir - Path to bmad directory
-   * @param {string} projectDir - Path to project directory
-   */
-  async buildStandaloneAgents(bmadDir, projectDir) {
-    const standaloneAgentsPath = path.join(bmadDir, 'agents');
-    const cfgAgentsDir = path.join(bmadDir, '_cfg', 'agents');
-
-    // Check if standalone agents directory exists
-    if (!(await fs.pathExists(standaloneAgentsPath))) {
-      return;
-    }
-
-    // Get all subdirectories in agents/
-    const agentDirs = await fs.readdir(standaloneAgentsPath, { withFileTypes: true });
-
-    for (const agentDir of agentDirs) {
-      if (!agentDir.isDirectory()) continue;
-
-      const agentDirPath = path.join(standaloneAgentsPath, agentDir.name);
-
-      // Find any .agent.yaml file in the directory
-      const files = await fs.readdir(agentDirPath);
-      const yamlFile = files.find((f) => f.endsWith('.agent.yaml'));
-
-      if (!yamlFile) continue;
-
-      const agentName = path.basename(yamlFile, '.agent.yaml');
-      const sourceYamlPath = path.join(agentDirPath, yamlFile);
-      const targetMdPath = path.join(agentDirPath, `${agentName}.md`);
-      const customizePath = path.join(cfgAgentsDir, `${agentName}.customize.yaml`);
-
-      // Check for customizations
-      const customizeExists = await fs.pathExists(customizePath);
-      let customizedFields = [];
-
-      if (customizeExists) {
-        const customizeContent = await fs.readFile(customizePath, 'utf8');
-        const yaml = require('js-yaml');
-        const customizeYaml = yaml.load(customizeContent);
-
-        // Detect what fields are customized (similar to rebuildAgentFiles)
-        if (customizeYaml) {
-          if (customizeYaml.persona) {
-            for (const [key, value] of Object.entries(customizeYaml.persona)) {
-              if (value !== '' && value !== null && !(Array.isArray(value) && value.length === 0)) {
-                customizedFields.push(`persona.${key}`);
-              }
-            }
-          }
-          if (customizeYaml.agent?.metadata) {
-            for (const [key, value] of Object.entries(customizeYaml.agent.metadata)) {
-              if (value !== '' && value !== null) {
-                customizedFields.push(`metadata.${key}`);
-              }
-            }
-          }
-          if (customizeYaml.critical_actions && customizeYaml.critical_actions.length > 0) {
-            customizedFields.push('critical_actions');
-          }
-          if (customizeYaml.menu && customizeYaml.menu.length > 0) {
-            customizedFields.push('menu');
-          }
-        }
-      }
-
-      // Build YAML to XML .md
-      const xmlContent = await this.xmlHandler.buildFromYaml(sourceYamlPath, customizeExists ? customizePath : null, {
-        includeMetadata: true,
-      });
-
-      // DO NOT replace {project-root} - LLMs understand this placeholder at runtime
-      // const processedContent = xmlContent.replaceAll('{project-root}', projectDir);
-
-      // Write the built .md file
-      await fs.writeFile(targetMdPath, xmlContent, 'utf8');
-
-      // Display result
-      if (customizedFields.length > 0) {
-        console.log(chalk.dim(`  Built standalone agent: ${agentName}.md `) + chalk.yellow(`(customized: ${customizedFields.join(', ')})`));
-      } else {
-        console.log(chalk.dim(`  Built standalone agent: ${agentName}.md`));
-      }
-    }
-  }
-
-  /**
-   * Rebuild agent files from installer source (for compile command)
-   * @param {string} modulePath - Path to module in bmad/ installation
-   * @param {string} moduleName - Module name
-   */
-  async rebuildAgentFiles(modulePath, moduleName) {
-    // Get source agents directory from installer
-    const sourceAgentsPath =
-      moduleName === 'core' ? path.join(getModulePath('core'), 'agents') : path.join(getSourcePath(`modules/${moduleName}`), 'agents');
-
-    if (!(await fs.pathExists(sourceAgentsPath))) {
-      return; // No source agents to rebuild
-    }
-
-    // Determine project directory (parent of bmad/ directory)
-    const bmadDir = path.dirname(modulePath);
-    const projectDir = path.dirname(bmadDir);
-    const cfgAgentsDir = path.join(bmadDir, '_cfg', 'agents');
-    const targetAgentsPath = path.join(modulePath, 'agents');
-
-    // Ensure target directory exists
-    await fs.ensureDir(targetAgentsPath);
-
-    // Get all YAML agent files from source
-    const sourceFiles = await fs.readdir(sourceAgentsPath);
-
-    for (const file of sourceFiles) {
-      if (file.endsWith('.agent.yaml')) {
-        const agentName = file.replace('.agent.yaml', '');
-        const sourceYamlPath = path.join(sourceAgentsPath, file);
-        const targetMdPath = path.join(targetAgentsPath, `${agentName}.md`);
-        const customizePath = path.join(cfgAgentsDir, `${moduleName}-${agentName}.customize.yaml`);
-
-        // Check for customizations
-        const customizeExists = await fs.pathExists(customizePath);
-        let customizedFields = [];
-
-        if (customizeExists) {
-          const customizeContent = await fs.readFile(customizePath, 'utf8');
-          const yaml = require('js-yaml');
-          const customizeYaml = yaml.load(customizeContent);
-
-          // Detect what fields are customized
-          if (customizeYaml) {
-            if (customizeYaml.persona) {
-              for (const [key, value] of Object.entries(customizeYaml.persona)) {
-                if (value !== '' && value !== null && !(Array.isArray(value) && value.length === 0)) {
-                  customizedFields.push(`persona.${key}`);
-                }
-              }
-            }
-            if (customizeYaml.agent?.metadata) {
-              for (const [key, value] of Object.entries(customizeYaml.agent.metadata)) {
-                if (value !== '' && value !== null) {
-                  customizedFields.push(`metadata.${key}`);
-                }
-              }
-            }
-            if (customizeYaml.critical_actions && customizeYaml.critical_actions.length > 0) {
-              customizedFields.push('critical_actions');
-            }
-            if (customizeYaml.memories && customizeYaml.memories.length > 0) {
-              customizedFields.push('memories');
-            }
-            if (customizeYaml.menu && customizeYaml.menu.length > 0) {
-              customizedFields.push('menu');
-            }
-            if (customizeYaml.prompts && customizeYaml.prompts.length > 0) {
-              customizedFields.push('prompts');
-            }
-          }
-        }
-
-        // Build YAML + customize to .md
-        const xmlContent = await this.xmlHandler.buildFromYaml(sourceYamlPath, customizeExists ? customizePath : null, {
-          includeMetadata: true,
-        });
-
-        // DO NOT replace {project-root} - LLMs understand this placeholder at runtime
-        // const processedContent = xmlContent.replaceAll('{project-root}', projectDir);
-
-        // Write the rebuilt .md file
-        await fs.writeFile(targetMdPath, xmlContent, 'utf8');
-
-        // Display result with customizations if any
-        if (customizedFields.length > 0) {
-          console.log(chalk.dim(`  Rebuilt agent: ${agentName}.md `) + chalk.yellow(`(customized: ${customizedFields.join(', ')})`));
-        } else {
-          console.log(chalk.dim(`  Rebuilt agent: ${agentName}.md`));
-        }
-      }
-    }
-  }
-
-  /**
-   * Compile/rebuild all agents and tasks for quick updates
-   * @param {Object} config - Compilation configuration
-   * @returns {Object} Compilation results
-   */
-  async compileAgents(config) {
-    const ora = require('ora');
-    const spinner = ora('Starting agent compilation...').start();
-
-    try {
-      const projectDir = path.resolve(config.directory);
-      const bmadDir = path.join(projectDir, 'bmad');
-
-      // Check if bmad directory exists
-      if (!(await fs.pathExists(bmadDir))) {
-        spinner.fail('No BMAD installation found');
-        throw new Error(`BMAD not installed at ${bmadDir}`);
-      }
-
-      let agentCount = 0;
-      let taskCount = 0;
-
-      // Process all modules in bmad directory
-      spinner.text = 'Rebuilding agent files...';
-      const entries = await fs.readdir(bmadDir, { withFileTypes: true });
-
-      for (const entry of entries) {
-        if (entry.isDirectory() && entry.name !== '_cfg' && entry.name !== 'docs') {
-          const modulePath = path.join(bmadDir, entry.name);
-
-          // Special handling for standalone agents in bmad/agents/ directory
-          if (entry.name === 'agents') {
-            spinner.text = 'Building standalone agents...';
-            await this.buildStandaloneAgents(bmadDir, projectDir);
-
-            // Count standalone agents
-            const standaloneAgentsPath = path.join(bmadDir, 'agents');
-            const standaloneAgentDirs = await fs.readdir(standaloneAgentsPath, { withFileTypes: true });
-            for (const agentDir of standaloneAgentDirs) {
-              if (agentDir.isDirectory()) {
-                const agentDirPath = path.join(standaloneAgentsPath, agentDir.name);
-                const agentFiles = await fs.readdir(agentDirPath);
-                agentCount += agentFiles.filter((f) => f.endsWith('.md') && !f.endsWith('.agent.yaml')).length;
-              }
-            }
-          } else {
-            // Rebuild module agents from installer source
-            const agentsPath = path.join(modulePath, 'agents');
-            if (await fs.pathExists(agentsPath)) {
-              await this.rebuildAgentFiles(modulePath, entry.name);
-              const agentFiles = await fs.readdir(agentsPath);
-              agentCount += agentFiles.filter((f) => f.endsWith('.md')).length;
-            }
-
-            // Count tasks (already built)
-            const tasksPath = path.join(modulePath, 'tasks');
-            if (await fs.pathExists(tasksPath)) {
-              const taskFiles = await fs.readdir(tasksPath);
-              taskCount += taskFiles.filter((f) => f.endsWith('.md')).length;
-            }
-          }
-        }
-      }
-
-      // Regenerate manifests after compilation
-      spinner.start('Regenerating manifests...');
-      const installedModules = entries
-        .filter((e) => e.isDirectory() && e.name !== '_cfg' && e.name !== 'docs' && e.name !== 'agents' && e.name !== 'core')
-        .map((e) => e.name);
-      const manifestGen = new ManifestGenerator();
-
-      // Get existing IDE list from manifest
-      const existingManifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
-      let existingIdes = [];
-      if (await fs.pathExists(existingManifestPath)) {
-        const manifestContent = await fs.readFile(existingManifestPath, 'utf8');
-        const yaml = require('js-yaml');
-        const manifest = yaml.load(manifestContent);
-        existingIdes = manifest.ides || [];
-      }
-
-      await manifestGen.generateManifests(bmadDir, installedModules, [], {
-        ides: existingIdes,
-      });
-      spinner.succeed('Manifests regenerated');
-
-      // Ask for IDE to update
-      spinner.stop();
-      // Note: UI lives in tools/cli/lib/ui.js; from installers/lib/core use '../../../lib/ui'
-      const { UI } = require('../../../lib/ui');
-      const ui = new UI();
-      const toolConfig = await ui.promptToolSelection(projectDir, []);
-
-      if (!toolConfig.skipIde && toolConfig.ides && toolConfig.ides.length > 0) {
-        spinner.start('Updating IDE configurations...');
-
-        for (const ide of toolConfig.ides) {
-          spinner.text = `Updating ${ide}...`;
-          await this.ideManager.setup(ide, projectDir, bmadDir, {
-            selectedModules: installedModules,
-            skipModuleInstall: true, // Skip module installation, just update IDE files
-            verbose: config.verbose,
-          });
-        }
-
-        spinner.succeed('IDE configurations updated');
-      }
-
-      return { agentCount, taskCount };
-    } catch (error) {
-      spinner.fail('Compilation failed');
-      throw error;
-    }
-  }
-
-  /**
-   * Private: Update core
+   * Private: Update core
    */
   async updateCore(bmadDir, force = false) {
     const sourcePath = getModulePath('core');
@@ -1528,6 +1827,12 @@ class Installer {
     } else {
       // Selective update - preserve user modifications
       await this.fileOps.syncDirectory(sourcePath, targetPath);
+
+      // Recompile agents (#1133)
+      const { ModuleManager } = require('../modules/manager');
+      const moduleManager = new ModuleManager();
+      await moduleManager.compileModuleAgents(sourcePath, targetPath, 'core', bmadDir, this);
+      await this.processAgentFiles(targetPath, 'core');
     }
   }
 
@@ -1542,7 +1847,7 @@ class Installer {
 
     try {
       const projectDir = path.resolve(config.directory);
-      const bmadDir = path.join(projectDir, 'bmad');
+      const { bmadDir } = await this.findBmadDir(projectDir);
 
       // Check if bmad directory exists
       if (!(await fs.pathExists(bmadDir))) {
@@ -1556,17 +1861,102 @@ class Installer {
       const existingInstall = await this.detector.detect(bmadDir);
       const installedModules = existingInstall.modules.map((m) => m.id);
       const configuredIdes = existingInstall.ides || [];
+      const projectRoot = path.dirname(bmadDir);
+
+      // Get custom module sources from cache
+      const customModuleSources = new Map();
+      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;
+
+            // Skip if we already have this module from manifest
+            if (customModuleSources.has(moduleId)) {
+              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)) {
+              // For quick update, we always rebuild from cache
+              customModuleSources.set(moduleId, {
+                id: moduleId,
+                name: moduleId, // We'll read the actual name if needed
+                sourcePath: cachedPath,
+                cached: true, // Flag to indicate this is from cache
+              });
+            }
+          }
+        }
+      }
 
       // Load saved IDE configurations
       const savedIdeConfigs = await this.ideConfigManager.loadAllIdeConfigs(bmadDir);
 
       // Get available modules (what we have source for)
-      const availableModules = await this.moduleManager.listAvailable();
-      const availableModuleIds = new Set(availableModules.map((m) => m.id));
+      const availableModulesData = await this.moduleManager.listAvailable();
+      const availableModules = [...availableModulesData.modules, ...availableModulesData.customModules];
+
+      // Add custom modules from manifest if their sources exist
+      for (const [moduleId, customModule] of customModuleSources) {
+        // Use the absolute sourcePath
+        const sourcePath = customModule.sourcePath;
+
+        // Check if source exists at the recorded path
+        if (
+          sourcePath &&
+          (await fs.pathExists(sourcePath)) && // Add to available modules if not already there
+          !availableModules.some((m) => m.id === moduleId)
+        ) {
+          availableModules.push({
+            id: moduleId,
+            name: customModule.name || moduleId,
+            path: sourcePath,
+            isCustom: true,
+            fromManifest: true,
+          });
+        }
+      }
+
+      // Handle missing custom module sources using shared method
+      const customModuleResult = await this.handleMissingCustomSources(
+        customModuleSources,
+        bmadDir,
+        projectRoot,
+        'update',
+        installedModules,
+      );
+
+      const { validCustomModules, keptModulesWithoutSources } = customModuleResult;
+
+      const customModulesFromManifest = validCustomModules.map((m) => ({
+        ...m,
+        isCustom: true,
+        hasUpdate: true,
+      }));
+
+      const allAvailableModules = [...availableModules, ...customModulesFromManifest];
+      const availableModuleIds = new Set(allAvailableModules.map((m) => m.id));
+
+      // Core module is special - never include it in update flow
+      const nonCoreInstalledModules = installedModules.filter((id) => id !== 'core');
 
       // Only update modules that are BOTH installed AND available (we have source for)
-      const modulesToUpdate = installedModules.filter((id) => availableModuleIds.has(id));
-      const skippedModules = installedModules.filter((id) => !availableModuleIds.has(id));
+      const modulesToUpdate = nonCoreInstalledModules.filter((id) => availableModuleIds.has(id));
+      const skippedModules = nonCoreInstalledModules.filter((id) => !availableModuleIds.has(id));
+
+      // Add custom modules that were kept without sources to the skipped modules
+      // This ensures their agents are preserved in the manifest
+      for (const keptModule of keptModulesWithoutSources) {
+        if (!skippedModules.includes(keptModule)) {
+          skippedModules.push(keptModule);
+        }
+      }
 
       spinner.succeed(`Found ${modulesToUpdate.length} module(s) to update and ${configuredIdes.length} configured tool(s)`);
 
@@ -1605,9 +1995,6 @@ class Installer {
         lastModified: new Date().toISOString(),
       };
 
-      // Now run the full installation with the collected configs
-      spinner.start('Updating BMAD installation...');
-
       // Build the config object for the installer
       const installConfig = {
         directory: projectDir,
@@ -1620,12 +2007,18 @@ class Installer {
         _quickUpdate: true, // Flag to skip certain prompts
         _preserveModules: skippedModules, // Preserve these in manifest even though we didn't update them
         _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
       };
 
       // Call the standard install method
       const result = await this.install(installConfig);
 
-      spinner.succeed('Quick update complete!');
+      // Only succeed the spinner if it's still spinning
+      // (install method might have stopped it if folder name changed)
+      if (spinner.isSpinning) {
+        spinner.succeed('Quick update complete!');
+      }
 
       return {
         success: true,
@@ -1641,6 +2034,108 @@ class Installer {
     }
   }
 
+  /**
+   * Compile agents with customizations only
+   * @param {Object} config - Configuration with directory
+   * @returns {Object} Compilation result
+   */
+  async compileAgents(config) {
+    const ora = require('ora');
+    const chalk = require('chalk');
+    const { ModuleManager } = require('../modules/manager');
+    const { getSourcePath } = require('../../../lib/project-root');
+
+    const spinner = ora('Recompiling agents with customizations...').start();
+
+    try {
+      const projectDir = path.resolve(config.directory);
+      const { bmadDir } = await this.findBmadDir(projectDir);
+
+      // Check if bmad directory exists
+      if (!(await fs.pathExists(bmadDir))) {
+        spinner.fail('No BMAD installation found');
+        throw new Error(`BMAD not installed at ${bmadDir}. Use regular install for first-time setup.`);
+      }
+
+      // Detect existing installation
+      const existingInstall = await this.detector.detect(bmadDir);
+      const installedModules = existingInstall.modules.map((m) => m.id);
+
+      // Initialize module manager
+      const moduleManager = new ModuleManager();
+      moduleManager.setBmadFolderName(path.basename(bmadDir));
+
+      let totalAgentCount = 0;
+
+      // Get custom module sources from cache
+      const customModuleSources = new Map();
+      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);
+            const moduleYamlPath = path.join(cachedPath, 'module.yaml');
+
+            // Check if this is actually a custom module
+            if (await fs.pathExists(moduleYamlPath)) {
+              customModuleSources.set(moduleId, cachedPath);
+            }
+          }
+        }
+      }
+
+      // Process each installed module
+      for (const moduleId of installedModules) {
+        spinner.text = `Recompiling agents in ${moduleId}...`;
+
+        // Get source path
+        let sourcePath;
+        if (moduleId === 'core') {
+          sourcePath = getSourcePath('core');
+        } else {
+          // First check if it's in the custom cache
+          if (customModuleSources.has(moduleId)) {
+            sourcePath = customModuleSources.get(moduleId);
+          } else {
+            sourcePath = await moduleManager.findModuleSource(moduleId);
+          }
+        }
+
+        if (!sourcePath) {
+          console.log(chalk.yellow(`  Warning: Source not found for module ${moduleId}, skipping...`));
+          continue;
+        }
+
+        const targetPath = path.join(bmadDir, moduleId);
+
+        // Compile agents for this module
+        await moduleManager.compileModuleAgents(sourcePath, targetPath, moduleId, bmadDir, this);
+
+        // Count agents (rough estimate based on files)
+        const agentsPath = path.join(targetPath, 'agents');
+        if (await fs.pathExists(agentsPath)) {
+          const agentFiles = await fs.readdir(agentsPath);
+          const agentCount = agentFiles.filter((f) => f.endsWith('.md')).length;
+          totalAgentCount += agentCount;
+        }
+      }
+
+      spinner.succeed('Agent recompilation complete!');
+
+      return {
+        success: true,
+        agentCount: totalAgentCount,
+        modules: installedModules,
+      };
+    } catch (error) {
+      spinner.fail('Agent recompilation failed');
+      throw error;
+    }
+  }
+
   /**
    * Private: Prompt for update action
    */
@@ -1651,11 +2146,7 @@ class Installer {
         type: 'list',
         name: 'action',
         message: 'What would you like to do?',
-        choices: [
-          { name: 'Update existing installation', value: 'update' },
-          { name: 'Remove and reinstall', value: 'reinstall' },
-          { name: 'Cancel', value: 'cancel' },
-        ],
+        choices: [{ name: 'Update existing installation', value: 'update' }],
       },
     ]);
   }
@@ -1669,14 +2160,14 @@ class Installer {
     console.log(chalk.yellow.bold('\n⚠️  Legacy BMAD v4 detected'));
     console.log(chalk.dim('The installer found legacy artefacts in your project.\n'));
 
-    // Separate .bmad* folders (auto-backup) from other offending paths (manual cleanup)
+    // Separate _bmad* folders (auto-backup) from other offending paths (manual cleanup)
     const bmadFolders = legacyV4.offenders.filter((p) => {
       const name = path.basename(p);
-      return name.startsWith('.bmad'); // Only dot-prefixed folders get auto-backed up
+      return name.startsWith('_bmad'); // Only dot-prefixed folders get auto-backed up
     });
     const otherOffenders = legacyV4.offenders.filter((p) => {
       const name = path.basename(p);
-      return !name.startsWith('.bmad'); // Everything else is manual cleanup
+      return !name.startsWith('_bmad'); // Everything else is manual cleanup
     });
 
     const inquirer = require('inquirer');
@@ -1709,7 +2200,7 @@ class Installer {
       }
     }
 
-    // Handle .bmad* folders with automatic backup
+    // Handle _bmad* folders with automatic backup
     if (bmadFolders.length > 0) {
       console.log(chalk.cyan('The following legacy folders will be moved to v4-backup:'));
       for (const p of bmadFolders) console.log(chalk.dim(` - ${p}`));
@@ -1753,7 +2244,7 @@ class Installer {
    * @returns {Array} Array of file entries from files-manifest.csv
    */
   async readFilesManifest(bmadDir) {
-    const filesManifestPath = path.join(bmadDir, '_cfg', 'files-manifest.csv');
+    const filesManifestPath = path.join(bmadDir, '_config', 'files-manifest.csv');
     if (!(await fs.pathExists(filesManifestPath))) {
       return [];
     }
@@ -1813,6 +2304,9 @@ class Installer {
     const customFiles = [];
     const modifiedFiles = [];
 
+    // Memory is always in _bmad/_memory
+    const bmadMemoryPath = '_memory';
+
     // Check if the manifest has hashes - if not, we can't detect modifications
     let manifestHasHashes = false;
     if (existingFilesManifest && existingFilesManifest.length > 0) {
@@ -1823,13 +2317,10 @@ class Installer {
     const installedFilesMap = new Map();
     for (const fileEntry of existingFilesManifest) {
       if (fileEntry.path) {
-        // Files in manifest are stored as relative paths starting with 'bmad/'
-        // Convert to absolute path
-        const relativePath = fileEntry.path.startsWith('bmad/') ? fileEntry.path.slice(5) : fileEntry.path;
-        const absolutePath = path.join(bmadDir, relativePath);
+        const absolutePath = path.join(bmadDir, fileEntry.path);
         installedFilesMap.set(path.normalize(absolutePath), {
           hash: fileEntry.hash,
-          relativePath: relativePath,
+          relativePath: fileEntry.path,
         });
       }
     }
@@ -1855,20 +2346,47 @@ class Installer {
             const relativePath = path.relative(bmadDir, fullPath);
             const fileName = path.basename(fullPath);
 
-            // Skip _cfg directory - system files
-            if (relativePath.startsWith('_cfg/') || relativePath.startsWith('_cfg\\')) {
+            // Skip _config directory EXCEPT for modified agent customizations
+            if (relativePath.startsWith('_config/') || relativePath.startsWith('_config\\')) {
+              // Special handling for .customize.yaml files - only preserve if modified
+              if (relativePath.includes('/agents/') && fileName.endsWith('.customize.yaml')) {
+                // Check if the customization file has been modified from manifest
+                const manifestPath = path.join(bmadDir, '_config', 'manifest.yaml');
+                if (await fs.pathExists(manifestPath)) {
+                  const crypto = require('node:crypto');
+                  const currentContent = await fs.readFile(fullPath, 'utf8');
+                  const currentHash = crypto.createHash('sha256').update(currentContent).digest('hex');
+
+                  const yaml = require('yaml');
+                  const manifestContent = await fs.readFile(manifestPath, 'utf8');
+                  const manifestData = yaml.parse(manifestContent);
+                  const originalHash = manifestData.agentCustomizations?.[relativePath];
+
+                  // Only add to customFiles if hash differs (user modified)
+                  if (originalHash && currentHash !== originalHash) {
+                    customFiles.push(fullPath);
+                  }
+                }
+              }
+              continue;
+            }
+
+            if (relativePath.startsWith(bmadMemoryPath + '/') && path.dirname(relativePath).includes('-sidecar')) {
               continue;
             }
 
             // Skip config.yaml files - these are regenerated on each install/update
-            // Users should use _cfg/agents/ override files instead
             if (fileName === 'config.yaml') {
               continue;
             }
 
             if (!fileInfo) {
               // File not in manifest = custom file
-              customFiles.push(fullPath);
+              // EXCEPT: Agent .md files in module folders are generated files, not custom
+              // Only treat .md files under _config/agents/ as custom
+              if (!(fileName.endsWith('.md') && relativePath.includes('/agents/') && !relativePath.startsWith('_config/'))) {
+                customFiles.push(fullPath);
+              }
             } else if (manifestHasHashes && fileInfo.hash) {
               // File in manifest with hash - check if it was modified
               const currentHash = await this.manifest.calculateFileHash(fullPath);
@@ -1880,8 +2398,6 @@ class Installer {
                 });
               }
             }
-            // If manifest doesn't have hashes, we can't detect modifications
-            // so we just skip files that are in the manifest
           }
         }
       } catch {
@@ -1894,201 +2410,240 @@ class Installer {
   }
 
   /**
-   * Private: Create agent configuration files
-   * @param {string} bmadDir - BMAD installation directory
-   * @param {Object} userInfo - User information including name and language
+   * Handle missing custom module sources interactively
+   * @param {Map} customModuleSources - Map of custom module ID to info
+   * @param {string} bmadDir - BMAD directory
+   * @param {string} projectRoot - Project root directory
+   * @param {string} operation - Current operation ('update', 'compile', etc.)
+   * @param {Array} installedModules - Array of installed module IDs (will be modified)
+   * @returns {Object} Object with validCustomModules array and keptModulesWithoutSources array
    */
-  async createAgentConfigs(bmadDir, userInfo = null) {
-    const agentConfigDir = path.join(bmadDir, '_cfg', 'agents');
-    await fs.ensureDir(agentConfigDir);
-
-    // Get all agents from all modules
-    const agents = [];
-    const agentDetails = []; // For manifest generation
-
-    // Check modules for agents (including core)
-    const entries = await fs.readdir(bmadDir, { withFileTypes: true });
-    for (const entry of entries) {
-      if (entry.isDirectory() && entry.name !== '_cfg') {
-        const moduleAgentsPath = path.join(bmadDir, entry.name, 'agents');
-        if (await fs.pathExists(moduleAgentsPath)) {
-          const agentFiles = await fs.readdir(moduleAgentsPath);
-          for (const agentFile of agentFiles) {
-            if (agentFile.endsWith('.md')) {
-              const agentPath = path.join(moduleAgentsPath, agentFile);
-              const agentContent = await fs.readFile(agentPath, 'utf8');
-
-              // Skip agents with localskip="true"
-              const hasLocalSkip = agentContent.match(/<agent[^>]*\slocalskip="true"[^>]*>/);
-              if (hasLocalSkip) {
-                continue; // Skip this agent - it should not have been installed
-              }
-
-              const agentName = path.basename(agentFile, '.md');
-
-              // Extract any nodes with agentConfig="true"
-              const agentConfigNodes = this.extractAgentConfigNodes(agentContent);
-
-              agents.push({
-                name: agentName,
-                module: entry.name,
-                agentConfigNodes: agentConfigNodes,
-              });
-
-              // Use shared AgentPartyGenerator to extract details
-              let details = AgentPartyGenerator.extractAgentDetails(agentContent, entry.name, agentName);
-
-              // Apply config overrides if they exist
-              if (details) {
-                const configPath = path.join(agentConfigDir, `${entry.name}-${agentName}.md`);
-                if (await fs.pathExists(configPath)) {
-                  const configContent = await fs.readFile(configPath, 'utf8');
-                  details = AgentPartyGenerator.applyConfigOverrides(details, configContent);
-                }
-                agentDetails.push(details);
-              }
-            }
-          }
+  async handleMissingCustomSources(customModuleSources, bmadDir, projectRoot, operation, installedModules) {
+    const validCustomModules = [];
+    const keptModulesWithoutSources = []; // Track modules kept without sources
+    const customModulesWithMissingSources = [];
+
+    // Check which sources exist
+    for (const [moduleId, customInfo] of customModuleSources) {
+      if (await fs.pathExists(customInfo.sourcePath)) {
+        validCustomModules.push({
+          id: moduleId,
+          name: customInfo.name,
+          path: customInfo.sourcePath,
+          info: customInfo,
+        });
+      } else {
+        // For cached modules that are missing, we just skip them without prompting
+        if (customInfo.cached) {
+          // Skip cached modules without prompting
+          keptModulesWithoutSources.push({
+            id: moduleId,
+            name: customInfo.name,
+            cached: true,
+          });
+        } else {
+          customModulesWithMissingSources.push({
+            id: moduleId,
+            name: customInfo.name,
+            sourcePath: customInfo.sourcePath,
+            relativePath: customInfo.relativePath,
+            info: customInfo,
+          });
         }
       }
     }
 
-    // Create config file for each agent
-    let createdCount = 0;
-    let skippedCount = 0;
-
-    // Load agent config template
-    const templatePath = getSourcePath('utility', 'models', 'agent-config-template.md');
-    const templateContent = await fs.readFile(templatePath, 'utf8');
+    // If no missing sources, return immediately
+    if (customModulesWithMissingSources.length === 0) {
+      return {
+        validCustomModules,
+        keptModulesWithoutSources: [],
+      };
+    }
 
-    for (const agent of agents) {
-      const configPath = path.join(agentConfigDir, `${agent.module}-${agent.name}.md`);
+    // Stop any spinner for interactive prompts
+    const currentSpinner = ora();
+    if (currentSpinner.isSpinning) {
+      currentSpinner.stop();
+    }
 
-      // Skip if config file already exists (preserve custom configurations)
-      if (await fs.pathExists(configPath)) {
-        skippedCount++;
-        continue;
-      }
+    console.log(chalk.yellow(`\n⚠️  Found ${customModulesWithMissingSources.length} custom module(s) with missing sources:`));
 
-      // Build config content header
-      let configContent = `# Agent Config: ${agent.name}\n\n`;
+    const inquirer = require('inquirer');
+    let keptCount = 0;
+    let updatedCount = 0;
+    let removedCount = 0;
 
-      // Process template and add agent-specific config nodes
-      let processedTemplate = templateContent;
+    for (const missing of customModulesWithMissingSources) {
+      console.log(chalk.dim(`  • ${missing.name} (${missing.id})`));
+      console.log(chalk.dim(`    Original source: ${missing.relativePath}`));
+      console.log(chalk.dim(`    Full path: ${missing.sourcePath}`));
 
-      // Replace {core:user_name} placeholder with actual user name if available
-      if (userInfo && userInfo.userName) {
-        processedTemplate = processedTemplate.replaceAll('{core:user_name}', userInfo.userName);
+      const choices = [
+        {
+          name: 'Keep installed (will not be processed)',
+          value: 'keep',
+          short: 'Keep',
+        },
+        {
+          name: 'Specify new source location',
+          value: 'update',
+          short: 'Update',
+        },
+      ];
+
+      // Only add remove option if not just compiling agents
+      if (operation !== 'compile-agents') {
+        choices.push({
+          name: '⚠️  REMOVE module completely (destructive!)',
+          value: 'remove',
+          short: 'Remove',
+        });
       }
 
-      // Replace {core:communication_language} placeholder with actual language if available
-      if (userInfo && userInfo.responseLanguage) {
-        processedTemplate = processedTemplate.replaceAll('{core:communication_language}', userInfo.responseLanguage);
-      }
+      const { action } = await inquirer.prompt([
+        {
+          type: 'list',
+          name: 'action',
+          message: `How would you like to handle "${missing.name}"?`,
+          choices,
+        },
+      ]);
 
-      // If this agent has agentConfig nodes, add them after the existing comment
-      if (agent.agentConfigNodes && agent.agentConfigNodes.length > 0) {
-        // Find the agent-specific configuration nodes comment
-        const commentPattern = /(\s*<!-- Agent-specific configuration nodes -->)/;
-        const commentMatch = processedTemplate.match(commentPattern);
+      switch (action) {
+        case 'update': {
+          const { newSourcePath } = await inquirer.prompt([
+            {
+              type: 'input',
+              name: 'newSourcePath',
+              message: 'Enter the new path to the custom module:',
+              default: missing.sourcePath,
+              validate: async (input) => {
+                if (!input || input.trim() === '') {
+                  return 'Please enter a path';
+                }
+                const expandedPath = path.resolve(input.trim());
+                if (!(await fs.pathExists(expandedPath))) {
+                  return 'Path does not exist';
+                }
+                // Check if it looks like a valid module
+                const moduleYamlPath = path.join(expandedPath, 'module.yaml');
+                const agentsPath = path.join(expandedPath, 'agents');
+                const workflowsPath = path.join(expandedPath, 'workflows');
 
-        if (commentMatch) {
-          // Add nodes right after the comment
-          let agentSpecificNodes = '';
-          for (const node of agent.agentConfigNodes) {
-            agentSpecificNodes += `\n    ${node}`;
-          }
+                if (!(await fs.pathExists(moduleYamlPath)) && !(await fs.pathExists(agentsPath)) && !(await fs.pathExists(workflowsPath))) {
+                  return 'Path does not appear to contain a valid custom module';
+                }
+                return true;
+              },
+            },
+          ]);
 
-          processedTemplate = processedTemplate.replace(commentPattern, `$1${agentSpecificNodes}`);
-        }
-      }
+          // Update the source in manifest
+          const resolvedPath = path.resolve(newSourcePath.trim());
+          missing.info.sourcePath = resolvedPath;
+          // Remove relativePath - we only store absolute sourcePath now
+          delete missing.info.relativePath;
+          await this.manifest.addCustomModule(bmadDir, missing.info);
+
+          validCustomModules.push({
+            id: missing.id,
+            name: missing.name,
+            path: resolvedPath,
+            info: missing.info,
+          });
 
-      configContent += processedTemplate;
+          updatedCount++;
+          console.log(chalk.green(`✓ Updated source location`));
 
-      await fs.writeFile(configPath, configContent, 'utf8');
-      this.installedFiles.push(configPath); // Track agent config files
-      createdCount++;
-    }
+          break;
+        }
+        case 'remove': {
+          // Extra confirmation for destructive remove
+          console.log(chalk.red.bold(`\n⚠️  WARNING: This will PERMANENTLY DELETE "${missing.name}" and all its files!`));
+          console.log(chalk.red(`  Module location: ${path.join(bmadDir, missing.id)}`));
 
-    // Generate agent manifest with overrides applied
-    await this.generateAgentManifest(bmadDir, agentDetails);
+          const { confirm } = await inquirer.prompt([
+            {
+              type: 'confirm',
+              name: 'confirm',
+              message: chalk.red.bold('Are you absolutely sure you want to delete this module?'),
+              default: false,
+            },
+          ]);
 
-    return { total: agents.length, created: createdCount, skipped: skippedCount };
-  }
+          if (confirm) {
+            const { typedConfirm } = await inquirer.prompt([
+              {
+                type: 'input',
+                name: 'typedConfirm',
+                message: chalk.red.bold('Type "DELETE" to confirm permanent deletion:'),
+                validate: (input) => {
+                  if (input !== 'DELETE') {
+                    return chalk.red('You must type "DELETE" exactly to proceed');
+                  }
+                  return true;
+                },
+              },
+            ]);
+
+            if (typedConfirm === 'DELETE') {
+              // Remove the module from filesystem and manifest
+              const modulePath = path.join(bmadDir, moduleId);
+              if (await fs.pathExists(modulePath)) {
+                const fsExtra = require('fs-extra');
+                await fsExtra.remove(modulePath);
+                console.log(chalk.yellow(`  ✓ Deleted module directory: ${path.relative(projectRoot, modulePath)}`));
+              }
 
-  /**
-   * Generate agent manifest XML file
-   * @param {string} bmadDir - BMAD installation directory
-   * @param {Array} agentDetails - Array of agent details
-   */
-  async generateAgentManifest(bmadDir, agentDetails) {
-    const manifestPath = path.join(bmadDir, '_cfg', 'agent-manifest.csv');
-    await AgentPartyGenerator.writeAgentParty(manifestPath, agentDetails, { forWeb: false });
-  }
+              await this.manifest.removeModule(bmadDir, moduleId);
+              await this.manifest.removeCustomModule(bmadDir, moduleId);
+              console.log(chalk.yellow(`  ✓ Removed from manifest`));
 
-  /**
-   * Extract nodes with agentConfig="true" from agent content
-   * @param {string} content - Agent file content
-   * @returns {Array} Array of XML nodes that should be added to agent config
-   */
-  extractAgentConfigNodes(content) {
-    const nodes = [];
+              // Also remove from installedModules list
+              if (installedModules && installedModules.includes(moduleId)) {
+                const index = installedModules.indexOf(moduleId);
+                if (index !== -1) {
+                  installedModules.splice(index, 1);
+                }
+              }
 
-    try {
-      // Find all XML nodes with agentConfig="true"
-      // Match self-closing tags and tags with content
-      const selfClosingPattern = /<([a-zA-Z][a-zA-Z0-9_-]*)\s+[^>]*agentConfig="true"[^>]*\/>/g;
-      const withContentPattern = /<([a-zA-Z][a-zA-Z0-9_-]*)\s+[^>]*agentConfig="true"[^>]*>([\s\S]*?)<\/\1>/g;
-
-      // Extract self-closing tags
-      let match;
-      while ((match = selfClosingPattern.exec(content)) !== null) {
-        // Extract just the tag without children (structure only)
-        const tagMatch = match[0].match(/<([a-zA-Z][a-zA-Z0-9_-]*)([^>]*)\/>/);
-        if (tagMatch) {
-          const tagName = tagMatch[1];
-          const attributes = tagMatch[2].replace(/\s*agentConfig="true"/, ''); // Remove agentConfig attribute
-          nodes.push(`<${tagName}${attributes}></${tagName}>`);
-        }
-      }
+              removedCount++;
+              console.log(chalk.red.bold(`✓ "${missing.name}" has been permanently removed`));
+            } else {
+              console.log(chalk.dim('  Removal cancelled - module will be kept'));
+              keptCount++;
+            }
+          } else {
+            console.log(chalk.dim('  Removal cancelled - module will be kept'));
+            keptCount++;
+          }
 
-      // Extract tags with content
-      while ((match = withContentPattern.exec(content)) !== null) {
-        const fullMatch = match[0];
-        const tagName = match[1];
+          break;
+        }
+        case 'keep': {
+          keptCount++;
+          keptModulesWithoutSources.push(moduleId);
+          console.log(chalk.dim(`  Module will be kept as-is`));
 
-        // Extract opening tag with attributes (removing agentConfig="true")
-        const openingTagMatch = fullMatch.match(new RegExp(`<${tagName}([^>]*)>`));
-        if (openingTagMatch) {
-          const attributes = openingTagMatch[1].replace(/\s*agentConfig="true"/, '');
-          // Add empty node structure (no children)
-          nodes.push(`<${tagName}${attributes}></${tagName}>`);
+          break;
         }
+        // No default
       }
-    } catch (error) {
-      console.error('Error extracting agentConfig nodes:', error);
     }
 
-    return nodes;
-  }
-
-  /**
-   * Copy IDE-specific documentation to BMAD docs
-   * @param {Array} ides - List of selected IDEs
-   * @param {string} bmadDir - BMAD installation directory
-   */
-  async copyIdeDocumentation(ides, bmadDir) {
-    const docsDir = path.join(bmadDir, 'docs');
-    await fs.ensureDir(docsDir);
-
-    for (const ide of ides) {
-      const sourceDocPath = path.join(getProjectRoot(), 'docs', 'ide-info', `${ide}.md`);
-      const targetDocPath = path.join(docsDir, `${ide}-instructions.md`);
-
-      if (await fs.pathExists(sourceDocPath)) {
-        await fs.copy(sourceDocPath, targetDocPath, { overwrite: true });
-      }
+    // Show summary
+    if (keptCount > 0 || updatedCount > 0 || removedCount > 0) {
+      console.log(chalk.dim(`\nSummary for custom modules with missing sources:`));
+      if (keptCount > 0) console.log(chalk.dim(`  • ${keptCount} module(s) kept as-is`));
+      if (updatedCount > 0) console.log(chalk.dim(`  • ${updatedCount} module(s) updated with new sources`));
+      if (removedCount > 0) console.log(chalk.red(`  • ${removedCount} module(s) permanently deleted`));
     }
+
+    return {
+      validCustomModules,
+      keptModulesWithoutSources,
+    };
   }
 }