bmad-elsabro 1.0.0

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

@@ -0,0 +1,2812 @@
+const path = require('node:path');
+const fs = require('fs-extra');
+const chalk = require('chalk');
+const ora = require('ora');
+const { Detector } = require('./detector');
+const { Manifest } = require('./manifest');
+const { ModuleManager } = require('../modules/manager');
+const { IdeManager } = require('../ide/manager');
+const { FileOps } = require('../../../lib/file-ops');
+const { Config } = require('../../../lib/config');
+const { XmlHandler } = require('../../../lib/xml-handler');
+const { DependencyResolver } = require('./dependency-resolver');
+const { ConfigCollector } = require('./config-collector');
+const { getProjectRoot, getSourcePath, getModulePath } = require('../../../lib/project-root');
+const { CLIUtils } = require('../../../lib/cli-utils');
+const { ManifestGenerator } = require('./manifest-generator');
+const { IdeConfigManager } = require('./ide-config-manager');
+const { CustomHandler } = require('../custom/handler');
+const prompts = require('../../../lib/prompts');
+
+// BMAD installation folder name - this is constant and should never change
+const BMAD_FOLDER_NAME = '_bmad';
+
+class Installer {
+  constructor() {
+    this.detector = new Detector();
+    this.manifest = new Manifest();
+    this.moduleManager = new ModuleManager();
+    this.ideManager = new IdeManager();
+    this.fileOps = new FileOps();
+    this.config = new Config();
+    this.xmlHandler = new XmlHandler();
+    this.dependencyResolver = new DependencyResolver();
+    this.configCollector = new ConfigCollector();
+    this.ideConfigManager = new IdeConfigManager();
+    this.installedFiles = new Set(); // Track all installed files
+    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
+   * @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 fs.readFile(), fs.writeFile(), fs.copy()
+   *
+
+   *
+   * 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');
+
+        // 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 });
+    }
+  }
+
+  /**
+   * Collect Tool/IDE configurations after module configuration
+   * @param {string} projectDir - Project directory
+   * @param {Array} selectedModules - Selected modules from configuration
+   * @param {boolean} isFullReinstall - Whether this is a full reinstall
+   * @param {Array} previousIdes - Previously configured IDEs (for reinstalls)
+   * @param {Array} preSelectedIdes - Pre-selected IDEs from early prompt (optional)
+   * @returns {Object} Tool/IDE selection and configurations
+   */
+  async collectToolConfigurations(projectDir, selectedModules, isFullReinstall = false, previousIdes = [], preSelectedIdes = null) {
+    // Use pre-selected IDEs if provided, otherwise prompt
+    let toolConfig;
+    if (preSelectedIdes === null) {
+      // Fallback: prompt for tool selection (backwards compatibility)
+      const { UI } = require('../../../lib/ui');
+      const ui = new UI();
+      toolConfig = await ui.promptToolSelection(projectDir);
+    } else {
+      // IDEs were already selected during initial prompts
+      toolConfig = {
+        ides: preSelectedIdes,
+        skipIde: !preSelectedIdes || preSelectedIdes.length === 0,
+      };
+    }
+
+    // Check for already configured IDEs
+    const { Detector } = require('./detector');
+    const detector = new Detector();
+    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
+    let previouslyConfiguredIdes;
+    if (isFullReinstall) {
+      // During reinstall, treat all IDEs as new (need configuration)
+      previouslyConfiguredIdes = [];
+    } else {
+      const existingInstall = await detector.detect(bmadDir);
+      previouslyConfiguredIdes = existingInstall.ides || [];
+    }
+
+    // Load saved IDE configurations for already-configured IDEs
+    const savedIdeConfigs = await this.ideConfigManager.loadAllIdeConfigs(bmadDir);
+
+    // Collect IDE-specific configurations if any were selected
+    const ideConfigurations = {};
+
+    // First, add saved configs for already-configured IDEs
+    for (const ide of toolConfig.ides || []) {
+      if (previouslyConfiguredIdes.includes(ide) && savedIdeConfigs[ide]) {
+        ideConfigurations[ide] = savedIdeConfigs[ide];
+      }
+    }
+
+    if (!toolConfig.skipIde && toolConfig.ides && toolConfig.ides.length > 0) {
+      // Ensure IDE manager is initialized
+      await this.ideManager.ensureInitialized();
+
+      // Determine which IDEs are newly selected (not previously configured)
+      const newlySelectedIdes = toolConfig.ides.filter((ide) => !previouslyConfiguredIdes.includes(ide));
+
+      if (newlySelectedIdes.length > 0) {
+        console.log('\n'); // Add spacing before IDE questions
+
+        // Collect configuration for IDEs that support it
+        for (const ide of newlySelectedIdes) {
+          try {
+            const handler = this.ideManager.handlers.get(ide);
+
+            if (!handler) {
+              console.warn(chalk.yellow(`Warning: IDE '${ide}' handler not found`));
+              continue;
+            }
+
+            // Check if this IDE handler has a collectConfiguration method
+            // (custom installers like Codex, Kilo, Kiro-cli may have this)
+            if (typeof handler.collectConfiguration === 'function') {
+              console.log(chalk.cyan(`\nConfiguring ${ide}...`));
+              ideConfigurations[ide] = await handler.collectConfiguration({
+                selectedModules: selectedModules || [],
+                projectDir,
+                bmadDir,
+              });
+            }
+            // Most config-driven IDEs don't need configuration - silently skip
+          } catch (error) {
+            // IDE doesn't support configuration or has an error
+            console.warn(chalk.yellow(`Warning: Could not load configuration for ${ide}: ${error.message}`));
+          }
+        }
+      }
+
+      // Log which IDEs are already configured and being kept
+      const keptIdes = toolConfig.ides.filter((ide) => previouslyConfiguredIdes.includes(ide));
+      if (keptIdes.length > 0) {
+        console.log(chalk.dim(`\nKeeping existing configuration for: ${keptIdes.join(', ')}`));
+      }
+    }
+
+    return {
+      ides: toolConfig.ides,
+      skipIde: toolConfig.skipIde,
+      configurations: ideConfigurations,
+    };
+  }
+
+  /**
+   * Main installation method
+   * @param {Object} config - Installation configuration
+   * @param {string} config.directory - Target directory
+   * @param {boolean} config.installCore - Whether to install core
+   * @param {string[]} config.modules - Modules to install
+   * @param {string[]} config.ides - IDEs to configure
+   * @param {boolean} config.skipIde - Skip IDE configuration
+   */
+  async install(originalConfig) {
+    // Clone config to avoid mutating the caller's object
+    const config = { ...originalConfig };
+
+    // Check if core config was already collected in UI
+    const hasCoreConfig = config.coreConfig && Object.keys(config.coreConfig).length > 0;
+
+    // Only display logo if core config wasn't already collected (meaning we're not continuing from UI)
+    if (!hasCoreConfig) {
+      // Display BMAD logo
+      CLIUtils.displayLogo();
+
+      // Display welcome message
+      CLIUtils.displaySection('BMad™  Installation', 'Version ' + require(path.join(getProjectRoot(), 'package.json')).version);
+    }
+
+    // Note: Legacy V4 detection now happens earlier in UI.promptInstall()
+    // before any config collection, so we don't need to check again here
+
+    const projectDir = path.resolve(config.directory);
+
+    // If core config was pre-collected (from interactive mode), use it
+    if (config.coreConfig && Object.keys(config.coreConfig).length > 0) {
+      this.configCollector.collectedConfig.core = config.coreConfig;
+      // Also store in allAnswers for cross-referencing
+      this.configCollector.allAnswers = {};
+      for (const [key, value] of Object.entries(config.coreConfig)) {
+        this.configCollector.allAnswers[`core_${key}`] = value;
+      }
+    }
+
+    // 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 {
+      // 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,
+        });
+      }
+    }
+
+    // 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();
+
+    try {
+      // 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...';
+        try {
+          // fs.ensureDir handles platform-specific directory creation
+          // It will recursively create all necessary parent directories
+          await fs.ensureDir(projectDir);
+        } catch (error) {
+          spinner.fail('Failed to create installation directory');
+          console.error(chalk.red(`Error: ${error.message}`));
+          // More detailed error for common issues
+          if (error.code === 'EACCES') {
+            console.error(chalk.red('Permission denied. Check parent directory permissions.'));
+          } else if (error.code === 'ENOSPC') {
+            console.error(chalk.red('No space left on device.'));
+          }
+          throw new Error(`Cannot create directory: ${projectDir}`);
+        }
+      }
+
+      // Check existing installation
+      spinner.text = 'Checking for existing installation...';
+      const existingInstall = await this.detector.detect(bmadDir);
+
+      if (existingInstall.installed && !config.force && !config._quickUpdate) {
+        spinner.stop();
+
+        // Check if user already decided what to do (from early menu in ui.js)
+        let action = null;
+        if (config.actionType === 'update') {
+          action = 'update';
+        } else {
+          // Fallback: Ask the user (backwards compatibility for other code paths)
+          console.log(chalk.yellow('\n⚠️  Existing BMAD installation detected'));
+          console.log(chalk.dim(`  Location: ${bmadDir}`));
+          console.log(chalk.dim(`  Version: ${existingInstall.version}`));
+
+          const promptResult = await this.promptUpdateAction();
+          action = promptResult.action;
+        }
+
+        if (action === 'update') {
+          // Store that we're updating for later processing
+          config._isUpdate = true;
+          config._existingInstall = existingInstall;
+
+          // Detect modules that were previously installed but are NOT in the new selection (to be removed)
+          const previouslyInstalledModules = new Set(existingInstall.modules.map((m) => m.id));
+          const newlySelectedModules = new Set(config.modules || []);
+
+          // Find modules to remove (installed but not in new selection)
+          // Exclude 'core' from being removable
+          const modulesToRemove = [...previouslyInstalledModules].filter((m) => !newlySelectedModules.has(m) && m !== 'core');
+
+          // If there are modules to remove, ask for confirmation
+          if (modulesToRemove.length > 0) {
+            const prompts = require('../../../lib/prompts');
+            spinner.stop();
+
+            console.log('');
+            console.log(chalk.yellow.bold('⚠️  Modules to be removed:'));
+            for (const moduleId of modulesToRemove) {
+              const moduleInfo = existingInstall.modules.find((m) => m.id === moduleId);
+              const displayName = moduleInfo?.name || moduleId;
+              const modulePath = path.join(bmadDir, moduleId);
+              console.log(chalk.red(`  - ${displayName} (${modulePath})`));
+            }
+            console.log('');
+
+            const confirmRemoval = await prompts.confirm({
+              message: `Remove ${modulesToRemove.length} module(s) from BMAD installation?`,
+              default: false,
+            });
+
+            if (confirmRemoval) {
+              // Remove module folders
+              for (const moduleId of modulesToRemove) {
+                const modulePath = path.join(bmadDir, moduleId);
+                try {
+                  if (await fs.pathExists(modulePath)) {
+                    await fs.remove(modulePath);
+                    console.log(chalk.dim(`  ✓ Removed: ${moduleId}`));
+                  }
+                } catch (error) {
+                  console.warn(chalk.yellow(`  Warning: Failed to remove ${moduleId}: ${error.message}`));
+                }
+              }
+              console.log(chalk.green(`  ✓ Removed ${modulesToRemove.length} module(s)`));
+            } else {
+              console.log(chalk.dim('  → Module removal cancelled'));
+              // Add the modules back to the selection since user cancelled removal
+              for (const moduleId of modulesToRemove) {
+                if (!config.modules) config.modules = [];
+                config.modules.push(moduleId);
+              }
+            }
+
+            spinner.start('Preparing update...');
+          }
+
+          // Detect custom and modified files BEFORE updating (compare current files vs files-manifest.csv)
+          const existingFilesManifest = await this.readFilesManifest(bmadDir);
+          const { customFiles, modifiedFiles } = await this.detectCustomFiles(bmadDir, existingFilesManifest);
+
+          config._customFiles = customFiles;
+          config._modifiedFiles = modifiedFiles;
+
+          // Preserve existing core configuration during updates
+          // Read the current core config.yaml to maintain user's settings
+          const coreConfigPath = path.join(bmadDir, 'core', 'config.yaml');
+          if ((await fs.pathExists(coreConfigPath)) && (!config.coreConfig || Object.keys(config.coreConfig).length === 0)) {
+            try {
+              const yaml = require('yaml');
+              const coreConfigContent = await fs.readFile(coreConfigPath, 'utf8');
+              const existingCoreConfig = yaml.parse(coreConfigContent);
+
+              // Store in config.coreConfig so it's preserved through the installation
+              config.coreConfig = existingCoreConfig;
+
+              // Also store in configCollector for use during config collection
+              this.configCollector.collectedConfig.core = existingCoreConfig;
+            } catch (error) {
+              console.warn(chalk.yellow(`Warning: Could not read existing core config: ${error.message}`));
+            }
+          }
+
+          // 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;
+                }
+
+                // Check if this is an external official module - skip cache for those
+                const isExternal = await this.moduleManager.isExternalModule(moduleId);
+                if (isExternal) {
+                  // External modules are handled via cloneExternalModule, not from cache
+                  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');
+            await fs.ensureDir(tempBackupDir);
+
+            spinner.start(`Backing up ${customFiles.length} custom files...`);
+            for (const customFile of customFiles) {
+              const relativePath = path.relative(bmadDir, customFile);
+              const backupPath = path.join(tempBackupDir, relativePath);
+              await fs.ensureDir(path.dirname(backupPath));
+              await fs.copy(customFile, backupPath);
+            }
+            spinner.succeed(`Backed up ${customFiles.length} custom files`);
+
+            config._tempBackupDir = tempBackupDir;
+          }
+
+          // 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');
+            await fs.ensureDir(tempModifiedBackupDir);
+
+            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);
+              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 if (existingInstall.installed && config._quickUpdate) {
+        // Quick update mode - automatically treat as update without prompting
+        spinner.text = 'Preparing quick update...';
+        config._isUpdate = true;
+        config._existingInstall = existingInstall;
+
+        // Detect custom and modified files BEFORE updating
+        const existingFilesManifest = await this.readFilesManifest(bmadDir);
+        const { customFiles, modifiedFiles } = await this.detectCustomFiles(bmadDir, existingFilesManifest);
+
+        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;
+              }
+
+              // Check if this is an external official module - skip cache for those
+              const isExternal = await this.moduleManager.isExternalModule(moduleId);
+              if (isExternal) {
+                // External modules are handled via cloneExternalModule, not from cache
+                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');
+          await fs.ensureDir(tempBackupDir);
+
+          spinner.start(`Backing up ${customFiles.length} custom files...`);
+          for (const customFile of customFiles) {
+            const relativePath = path.relative(bmadDir, customFile);
+            const backupPath = path.join(tempBackupDir, relativePath);
+            await fs.ensureDir(path.dirname(backupPath));
+            await fs.copy(customFile, backupPath);
+          }
+          spinner.succeed(`Backed up ${customFiles.length} custom files`);
+          config._tempBackupDir = tempBackupDir;
+        }
+
+        // Back up modified files
+        if (modifiedFiles.length > 0) {
+          const tempModifiedBackupDir = path.join(projectDir, '_bmad-modified-backup-temp');
+          await fs.ensureDir(tempModifiedBackupDir);
+
+          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);
+            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;
+        }
+      }
+
+      // Now collect tool configurations after we know if it's a reinstall
+      // Skip for quick update since we already have the IDE list
+      spinner.stop();
+      let toolSelection;
+      if (config._quickUpdate) {
+        // Quick update already has IDEs configured, use saved configurations
+        const preConfiguredIdes = {};
+        const savedIdeConfigs = config._savedIdeConfigs || {};
+
+        for (const ide of config.ides || []) {
+          // Use saved config if available, otherwise mark as already configured (legacy)
+          if (savedIdeConfigs[ide]) {
+            preConfiguredIdes[ide] = savedIdeConfigs[ide];
+          } else {
+            preConfiguredIdes[ide] = { _alreadyConfigured: true };
+          }
+        }
+        toolSelection = {
+          ides: config.ides || [],
+          skipIde: !config.ides || config.ides.length === 0,
+          configurations: preConfiguredIdes,
+        };
+      } else {
+        // Pass pre-selected IDEs from early prompt (if available)
+        // This allows IDE selection to happen before file copying, improving UX
+        const preSelectedIdes = config.ides && config.ides.length > 0 ? config.ides : null;
+        toolSelection = await this.collectToolConfigurations(
+          path.resolve(config.directory),
+          config.modules,
+          config._isFullReinstall || false,
+          config._previouslyConfiguredIdes || [],
+          preSelectedIdes,
+        );
+      }
+
+      // Merge tool selection into config (for both quick update and regular flow)
+      config.ides = toolSelection.ides;
+      config.skipIde = toolSelection.skipIde;
+      const ideConfigurations = toolSelection.configurations;
+
+      // Add spacing after prompts before installation progress
+      console.log('');
+
+      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);
+
+      // 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 (const [moduleId, sourcePath] of customModulePaths) {
+          const cachedInfo = await customCache.cacheModule(moduleId, sourcePath, {
+            sourcePath: sourcePath, // Store original path for updates
+          });
+
+          // 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');
+      }
+
+      const projectRoot = getProjectRoot();
+
+      // Step 1: Install core module first (if requested)
+      if (config.installCore) {
+        spinner.start('Installing BMAD 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 (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 (!allModules.includes(module) && module !== 'core') {
+            const totalFiles =
+              files.agents.length +
+              files.tasks.length +
+              files.tools.length +
+              files.templates.length +
+              files.data.length +
+              files.other.length;
+            if (totalFiles > 0) {
+              spinner.start(`Installing ${module} dependencies...`);
+              await this.installPartialModule(module, bmadDir, files);
+              spinner.succeed(`${module} dependencies installed`);
+            }
+          }
+        }
+      }
+
+      // 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);
+      spinner.succeed('Module configurations generated');
+
+      // Create agent configuration files
+      // Note: Legacy createAgentConfigs removed - using YAML customize system instead
+      // 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, '_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
+      // This must happen BEFORE mergeModuleHelpCatalogs because it depends on agent-manifest.csv
+      spinner.start('Generating workflow and agent manifests...');
+      const manifestGen = new ManifestGenerator();
+
+      // 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, allModulesForManifest, [...this.installedFiles], {
+        ides: config.ides || [],
+        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`,
+      );
+
+      // Merge all module-help.csv files into bmad-help.csv
+      // This must happen AFTER generateManifests because it depends on agent-manifest.csv
+      spinner.start('Generating workflow help catalog...');
+      await this.mergeModuleHelpCatalogs(bmadDir);
+      spinner.succeed('Workflow help catalog generated');
+
+      // Configure IDEs and copy documentation
+      if (!config.skipIde && config.ides && config.ides.length > 0) {
+        // Ensure IDE manager is initialized (handlers may not be loaded in quick update flow)
+        await this.ideManager.ensureInitialized();
+
+        // Filter out any undefined/null values from the IDE list
+        const validIdes = config.ides.filter((ide) => ide && typeof ide === 'string');
+
+        if (validIdes.length === 0) {
+          console.log(chalk.yellow('⚠️  No valid IDEs selected. Skipping IDE configuration.'));
+        } else {
+          // Check if any IDE might need prompting (no pre-collected config)
+          const needsPrompting = validIdes.some((ide) => !ideConfigurations[ide]);
+
+          if (!needsPrompting) {
+            spinner.start('Configuring IDEs...');
+          }
+
+          // Temporarily suppress console output if not verbose
+          const originalLog = console.log;
+          if (!config.verbose) {
+            console.log = () => {};
+          }
+
+          for (const ide of validIdes) {
+            // Only show spinner if we have pre-collected config (no prompts expected)
+            if (ideConfigurations[ide] && !needsPrompting) {
+              spinner.text = `Configuring ${ide}...`;
+            } else if (!ideConfigurations[ide]) {
+              // Stop spinner before prompting
+              if (spinner.isSpinning) {
+                spinner.stop();
+              }
+              console.log(chalk.cyan(`\nConfiguring ${ide}...`));
+            }
+
+            // Pass pre-collected configuration to avoid re-prompting
+            await this.ideManager.setup(ide, projectDir, bmadDir, {
+              selectedModules: allModules || [],
+              preCollectedConfig: ideConfigurations[ide] || null,
+              verbose: config.verbose,
+            });
+
+            // Save IDE configuration for future updates
+            if (ideConfigurations[ide] && !ideConfigurations[ide]._alreadyConfigured) {
+              await this.ideConfigManager.saveIdeConfig(bmadDir, ide, ideConfigurations[ide]);
+            }
+
+            // Restart spinner if we stopped it
+            if (!ideConfigurations[ide] && !spinner.isSpinning) {
+              spinner.start('Configuring IDEs...');
+            }
+          }
+
+          // Restore console.log
+          console.log = originalLog;
+
+          if (spinner.isSpinning) {
+            spinner.succeed(`Configured: ${validIdes.join(', ')}`);
+          } else {
+            console.log(chalk.green(`✓ Configured: ${validIdes.join(', ')}`));
+          }
+        }
+      }
+
+      // 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...';
+
+        await this.moduleManager.runModuleInstaller('core', bmadDir, {
+          installedIDEs: config.ides || [],
+          moduleConfig: moduleConfigs.core || {},
+          coreConfig: moduleConfigs.core || {},
+          logger: moduleLogger,
+        });
+      }
+
+      // Run installers for user-selected modules
+      if (config.modules && config.modules.length > 0) {
+        for (const moduleName of config.modules) {
+          spinner.text = `Running ${moduleName} module installer...`;
+
+          // Pass installed IDEs and module config to module installer
+          await this.moduleManager.runModuleInstaller(moduleName, bmadDir, {
+            installedIDEs: config.ides || [],
+            moduleConfig: moduleConfigs[moduleName] || {},
+            coreConfig: moduleConfigs.core || {},
+            logger: moduleLogger,
+          });
+        }
+      }
+
+      spinner.succeed('Module-specific installers completed');
+
+      // Note: Manifest files are already created by ManifestGenerator above
+      // No need to create legacy manifest.csv anymore
+
+      // If this was an update, restore custom files
+      let customFiles = [];
+      let modifiedFiles = [];
+      if (config._isUpdate) {
+        if (config._customFiles && config._customFiles.length > 0) {
+          spinner.start(`Restoring ${config._customFiles.length} custom files...`);
+
+          for (const originalPath of config._customFiles) {
+            const relativePath = path.relative(bmadDir, originalPath);
+            const backupPath = path.join(config._tempBackupDir, relativePath);
+
+            if (await fs.pathExists(backupPath)) {
+              await fs.ensureDir(path.dirname(originalPath));
+              await fs.copy(backupPath, originalPath, { overwrite: true });
+            }
+          }
+
+          // Clean up temp backup
+          if (config._tempBackupDir && (await fs.pathExists(config._tempBackupDir))) {
+            await fs.remove(config._tempBackupDir);
+          }
+
+          spinner.succeed(`Restored ${config._customFiles.length} custom files`);
+          customFiles = config._customFiles;
+        }
+
+        if (config._modifiedFiles && config._modifiedFiles.length > 0) {
+          modifiedFiles = config._modifiedFiles;
+
+          // Restore modified files as .bak files
+          if (config._tempModifiedBackupDir && (await fs.pathExists(config._tempModifiedBackupDir))) {
+            spinner.start(`Restoring ${modifiedFiles.length} modified files as .bak...`);
+
+            for (const modifiedFile of modifiedFiles) {
+              const relativePath = path.relative(bmadDir, modifiedFile.path);
+              const tempBackupPath = path.join(config._tempModifiedBackupDir, relativePath);
+              const bakPath = modifiedFile.path + '.bak';
+
+              if (await fs.pathExists(tempBackupPath)) {
+                await fs.ensureDir(path.dirname(bakPath));
+                await fs.copy(tempBackupPath, bakPath, { overwrite: true });
+              }
+            }
+
+            // Clean up temp backup
+            await fs.remove(config._tempModifiedBackupDir);
+
+            spinner.succeed(`Restored ${modifiedFiles.length} modified files as .bak`);
+          }
+        }
+      }
+
+      spinner.stop();
+
+      // Report custom and modified files if any were found
+      if (customFiles.length > 0) {
+        console.log(chalk.cyan(`\n📁 Custom files preserved: ${customFiles.length}`));
+      }
+
+      if (modifiedFiles.length > 0) {
+        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
+      const { UI } = require('../../../lib/ui');
+      const ui = new UI();
+      ui.showInstallSummary({
+        path: bmadDir,
+        modules: config.modules,
+        ides: config.ides,
+        customFiles: customFiles.length > 0 ? customFiles : undefined,
+      });
+
+      return {
+        success: true,
+        path: bmadDir,
+        modules: config.modules,
+        ides: config.ides,
+        projectDir: projectDir,
+      };
+    } catch (error) {
+      spinner.fail('Installation failed');
+      throw error;
+    }
+  }
+
+  /**
+   * Update existing installation
+   */
+  async update(config) {
+    const spinner = ora('Checking installation...').start();
+
+    try {
+      const projectDir = path.resolve(config.directory);
+      const { bmadDir } = await this.findBmadDir(projectDir);
+      const existingInstall = await this.detector.detect(bmadDir);
+
+      if (!existingInstall.installed) {
+        spinner.fail('No BMAD installation found');
+        throw new Error(`No BMAD installation found at ${bmadDir}`);
+      }
+
+      spinner.text = 'Analyzing update requirements...';
+
+      // Compare versions and determine what needs updating
+      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;
+            }
+
+            // Check if this is an external official module - skip cache for those
+            const isExternal = await this.moduleManager.isExternalModule(moduleId);
+            if (isExternal) {
+              // External modules are handled via cloneExternalModule, not from cache
+              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'));
+        console.log(chalk.bold('Current version:'), currentVersion);
+        console.log(chalk.bold('New version:'), newVersion);
+        console.log(chalk.bold('Core:'), existingInstall.hasCore ? 'Will be updated' : 'Not installed');
+
+        if (existingInstall.modules.length > 0) {
+          console.log(chalk.bold('\nModules to update:'));
+          for (const mod of existingInstall.modules) {
+            console.log(`  - ${mod.id}`);
+          }
+        }
+        return;
+      }
+
+      // Perform actual update
+      if (existingInstall.hasCore) {
+        spinner.text = 'Updating core...';
+        await this.updateCore(bmadDir, config.force);
+      }
+
+      for (const module of existingInstall.modules) {
+        spinner.text = `Updating module: ${module.id}...`;
+        await this.moduleManager.update(module.id, bmadDir, config.force);
+      }
+
+      // Update manifest
+      spinner.text = 'Updating manifest...';
+      await this.manifest.update(bmadDir, {
+        version: newVersion,
+        updateDate: new Date().toISOString(),
+      });
+
+      spinner.succeed('Update complete');
+      return { success: true };
+    } catch (error) {
+      spinner.fail('Update failed');
+      throw error;
+    }
+  }
+
+  /**
+   * Get installation status
+   */
+  async getStatus(directory) {
+    const projectDir = path.resolve(directory);
+    const { bmadDir } = await this.findBmadDir(projectDir);
+    return await this.detector.detect(bmadDir);
+  }
+
+  /**
+   * Get available modules
+   */
+  async getAvailableModules() {
+    return await this.moduleManager.listAvailable();
+  }
+
+  /**
+   * Uninstall BMAD
+   */
+  async uninstall(directory) {
+    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(projectDir);
+
+    return { success: true };
+  }
+
+  /**
+   * Private: Create directory structure
+   */
+  /**
+   * Merge all module-help.csv files into a single bmad-help.csv
+   * Scans all installed modules for module-help.csv and merges them
+   * Enriches agent info from agent-manifest.csv
+   * Output is written to _bmad/_config/bmad-help.csv
+   * @param {string} bmadDir - BMAD installation directory
+   */
+  async mergeModuleHelpCatalogs(bmadDir) {
+    const allRows = [];
+    const headerRow =
+      'module,phase,name,code,sequence,workflow-file,command,required,agent-name,agent-command,agent-display-name,agent-title,options,description,output-location,outputs';
+
+    // Load agent manifest for agent info lookup
+    const agentManifestPath = path.join(bmadDir, '_config', 'agent-manifest.csv');
+    const agentInfo = new Map(); // agent-name -> {command, displayName, title+icon}
+
+    if (await fs.pathExists(agentManifestPath)) {
+      const manifestContent = await fs.readFile(agentManifestPath, 'utf8');
+      const lines = manifestContent.split('\n').filter((line) => line.trim());
+
+      for (const line of lines) {
+        if (line.startsWith('name,')) continue; // Skip header
+
+        const cols = line.split(',');
+        if (cols.length >= 4) {
+          const agentName = cols[0].replaceAll('"', '').trim();
+          const displayName = cols[1].replaceAll('"', '').trim();
+          const title = cols[2].replaceAll('"', '').trim();
+          const icon = cols[3].replaceAll('"', '').trim();
+          const module = cols[10] ? cols[10].replaceAll('"', '').trim() : '';
+
+          // Build agent command: bmad:module:agent:name
+          const agentCommand = module ? `bmad:${module}:agent:${agentName}` : `bmad:agent:${agentName}`;
+
+          agentInfo.set(agentName, {
+            command: agentCommand,
+            displayName: displayName || agentName,
+            title: icon && title ? `${icon} ${title}` : title || agentName,
+          });
+        }
+      }
+    }
+
+    // Get all installed module directories
+    const entries = await fs.readdir(bmadDir, { withFileTypes: true });
+    const installedModules = entries
+      .filter((entry) => entry.isDirectory() && entry.name !== '_config' && entry.name !== 'docs' && entry.name !== '_memory')
+      .map((entry) => entry.name);
+
+    // Add core module to scan (it's installed at root level as _config, but we check src/core)
+    const coreModulePath = getSourcePath('core');
+    const modulePaths = new Map();
+
+    // Map all module source paths
+    if (await fs.pathExists(coreModulePath)) {
+      modulePaths.set('core', coreModulePath);
+    }
+
+    // Map installed module paths
+    for (const moduleName of installedModules) {
+      const modulePath = path.join(bmadDir, moduleName);
+      modulePaths.set(moduleName, modulePath);
+    }
+
+    // Scan each module for module-help.csv
+    for (const [moduleName, modulePath] of modulePaths) {
+      const helpFilePath = path.join(modulePath, 'module-help.csv');
+
+      if (await fs.pathExists(helpFilePath)) {
+        try {
+          const content = await fs.readFile(helpFilePath, 'utf8');
+          const lines = content.split('\n').filter((line) => line.trim() && !line.startsWith('#'));
+
+          for (const line of lines) {
+            // Skip header row
+            if (line.startsWith('module,')) {
+              continue;
+            }
+
+            // Parse the line - handle quoted fields with commas
+            const columns = this.parseCSVLine(line);
+            if (columns.length >= 12) {
+              // Map old schema to new schema
+              // Old: module,phase,name,code,sequence,workflow-file,command,required,agent,options,description,output-location,outputs
+              // New: module,phase,name,code,sequence,workflow-file,command,required,agent-name,agent-command,agent-display-name,agent-title,options,description,output-location,outputs
+
+              const [
+                module,
+                phase,
+                name,
+                code,
+                sequence,
+                workflowFile,
+                command,
+                required,
+                agentName,
+                options,
+                description,
+                outputLocation,
+                outputs,
+              ] = columns;
+
+              // If module column is empty, set it to this module's name (except for core which stays empty for universal tools)
+              const finalModule = (!module || module.trim() === '') && moduleName !== 'core' ? moduleName : module || '';
+
+              // Lookup agent info
+              const cleanAgentName = agentName ? agentName.trim() : '';
+              const agentData = agentInfo.get(cleanAgentName) || { command: '', displayName: '', title: '' };
+
+              // Build new row with agent info
+              const newRow = [
+                finalModule,
+                phase || '',
+                name || '',
+                code || '',
+                sequence || '',
+                workflowFile || '',
+                command || '',
+                required || 'false',
+                cleanAgentName,
+                agentData.command,
+                agentData.displayName,
+                agentData.title,
+                options || '',
+                description || '',
+                outputLocation || '',
+                outputs || '',
+              ];
+
+              allRows.push(newRow.map((c) => this.escapeCSVField(c)).join(','));
+            }
+          }
+
+          if (process.env.BMAD_VERBOSE_INSTALL === 'true') {
+            console.log(chalk.dim(`  Merged module-help from: ${moduleName}`));
+          }
+        } catch (error) {
+          console.warn(chalk.yellow(`  Warning: Failed to read module-help.csv from ${moduleName}:`, error.message));
+        }
+      }
+    }
+
+    // Sort by module, then phase, then sequence
+    allRows.sort((a, b) => {
+      const colsA = this.parseCSVLine(a);
+      const colsB = this.parseCSVLine(b);
+
+      // Module comparison (empty module/universal tools come first)
+      const moduleA = (colsA[0] || '').toLowerCase();
+      const moduleB = (colsB[0] || '').toLowerCase();
+      if (moduleA !== moduleB) {
+        return moduleA.localeCompare(moduleB);
+      }
+
+      // Phase comparison
+      const phaseA = colsA[1] || '';
+      const phaseB = colsB[1] || '';
+      if (phaseA !== phaseB) {
+        return phaseA.localeCompare(phaseB);
+      }
+
+      // Sequence comparison
+      const seqA = parseInt(colsA[4] || '0', 10);
+      const seqB = parseInt(colsB[4] || '0', 10);
+      return seqA - seqB;
+    });
+
+    // Write merged catalog
+    const outputDir = path.join(bmadDir, '_config');
+    await fs.ensureDir(outputDir);
+    const outputPath = path.join(outputDir, 'bmad-help.csv');
+
+    const mergedContent = [headerRow, ...allRows].join('\n');
+    await fs.writeFile(outputPath, mergedContent, 'utf8');
+
+    // Track the installed file
+    this.installedFiles.add(outputPath);
+
+    if (process.env.BMAD_VERBOSE_INSTALL === 'true') {
+      console.log(chalk.dim(`  Generated bmad-help.csv: ${allRows.length} workflows`));
+    }
+  }
+
+  /**
+   * Parse a CSV line, handling quoted fields
+   * @param {string} line - CSV line to parse
+   * @returns {Array} Array of field values
+   */
+  parseCSVLine(line) {
+    const result = [];
+    let current = '';
+    let inQuotes = false;
+
+    for (let i = 0; i < line.length; i++) {
+      const char = line[i];
+      const nextChar = line[i + 1];
+
+      if (char === '"') {
+        if (inQuotes && nextChar === '"') {
+          // Escaped quote
+          current += '"';
+          i++; // Skip next quote
+        } else {
+          // Toggle quote mode
+          inQuotes = !inQuotes;
+        }
+      } else if (char === ',' && !inQuotes) {
+        result.push(current);
+        current = '';
+      } else {
+        current += char;
+      }
+    }
+    result.push(current);
+    return result;
+  }
+
+  /**
+   * Escape a CSV field if it contains special characters
+   * @param {string} field - Field value to escape
+   * @returns {string} Escaped field
+   */
+  escapeCSVField(field) {
+    if (field === null || field === undefined) {
+      return '';
+    }
+    const str = String(field);
+    // If field contains comma, quote, or newline, wrap in quotes and escape inner quotes
+    if (str.includes(',') || str.includes('"') || str.includes('\n')) {
+      return `"${str.replaceAll('"', '""')}"`;
+    }
+    return str;
+  }
+
+  async createDirectoryStructure(bmadDir) {
+    await fs.ensureDir(bmadDir);
+    await fs.ensureDir(path.join(bmadDir, '_config'));
+    await fs.ensureDir(path.join(bmadDir, '_config', 'agents'));
+    await fs.ensureDir(path.join(bmadDir, '_config', 'custom'));
+  }
+
+  /**
+   * Generate clean config.yaml files for each installed module
+   * @param {string} bmadDir - BMAD installation directory
+   * @param {Object} moduleConfigs - Collected configuration values
+   */
+  async generateModuleConfigs(bmadDir, moduleConfigs) {
+    const yaml = require('yaml');
+
+    // Extract core config values to share with other modules
+    const coreConfig = moduleConfigs.core || {};
+
+    // Get all installed module directories
+    const entries = await fs.readdir(bmadDir, { withFileTypes: true });
+    const installedModules = entries
+      .filter((entry) => entry.isDirectory() && entry.name !== '_config' && entry.name !== 'docs')
+      .map((entry) => entry.name);
+
+    // Generate config.yaml for each installed module
+    for (const moduleName of installedModules) {
+      const modulePath = path.join(bmadDir, moduleName);
+
+      // Get module-specific config or use empty object if none
+      const config = moduleConfigs[moduleName] || {};
+
+      if (await fs.pathExists(modulePath)) {
+        const configPath = path.join(modulePath, 'config.yaml');
+
+        // Create header
+        const packageJson = require(path.join(getProjectRoot(), 'package.json'));
+        const header = `# ${moduleName.toUpperCase()} Module Configuration
+# Generated by BMAD installer
+# Version: ${packageJson.version}
+# Date: ${new Date().toISOString()}
+
+`;
+
+        // For non-core modules, add core config values directly
+        let finalConfig = { ...config };
+        let coreSection = '';
+
+        if (moduleName !== 'core' && coreConfig && Object.keys(coreConfig).length > 0) {
+          // Add core values directly to the module config
+          // These will be available for reference in the module
+          finalConfig = {
+            ...config,
+            ...coreConfig, // Spread core config values directly into the module config
+          };
+
+          // Create a comment section to identify core values
+          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.stringify(cleanConfig, {
+          indent: 2,
+          lineWidth: 0,
+          minContentWidth: 0,
+        });
+
+        // If we have core values, reorganize the YAML to group them with their comment
+        if (coreSection && moduleName !== 'core') {
+          // Split the YAML into lines
+          const lines = yamlContent.split('\n');
+          const moduleConfigLines = [];
+          const coreConfigLines = [];
+
+          // Separate module-specific and core config lines
+          for (const line of lines) {
+            const key = line.split(':')[0].trim();
+            if (Object.prototype.hasOwnProperty.call(coreConfig, key)) {
+              coreConfigLines.push(line);
+            } else {
+              moduleConfigLines.push(line);
+            }
+          }
+
+          // Rebuild YAML with module config first, then core config with comment
+          yamlContent = moduleConfigLines.join('\n');
+          if (coreConfigLines.length > 0) {
+            yamlContent += coreSection + coreConfigLines.join('\n');
+          }
+        }
+
+        // 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.add(configPath);
+      }
+    }
+  }
+
+  /**
+   * Install core with resolved dependencies
+   * @param {string} bmadDir - BMAD installation directory
+   * @param {Object} coreFiles - Core files to install
+   */
+  async installCoreWithDependencies(bmadDir, coreFiles) {
+    const sourcePath = getModulePath('core');
+    const targetPath = path.join(bmadDir, 'core');
+    await this.installCore(bmadDir);
+  }
+
+  /**
+   * Install module with resolved dependencies
+   * @param {string} moduleName - Module name
+   * @param {string} bmadDir - BMAD installation directory
+   * @param {Object} moduleFiles - Module files to install
+   */
+  async installModuleWithDependencies(moduleName, bmadDir, moduleFiles) {
+    // Get module configuration for conditional installation
+    const moduleConfig = this.configCollector.collectedConfig[moduleName] || {};
+
+    // Use existing module manager for full installation with file tracking
+    // Note: Module-specific installers are called separately after IDE setup
+    await this.moduleManager.install(
+      moduleName,
+      bmadDir,
+      (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,
+      },
+    );
+
+    // Process agent files to build YAML agents and create customize templates
+    const modulePath = path.join(bmadDir, moduleName);
+    await this.processAgentFiles(modulePath, moduleName);
+
+    // Dependencies are already included in full module install
+  }
+
+  /**
+   * Install partial module (only dependencies needed by other modules)
+   */
+  async installPartialModule(moduleName, bmadDir, files) {
+    const sourceBase = getModulePath(moduleName);
+    const targetBase = path.join(bmadDir, moduleName);
+
+    // Create module directory
+    await fs.ensureDir(targetBase);
+
+    // Copy only the required dependency files
+    if (files.agents && files.agents.length > 0) {
+      const agentsDir = path.join(targetBase, 'agents');
+      await fs.ensureDir(agentsDir);
+
+      for (const agentPath of files.agents) {
+        const fileName = path.basename(agentPath);
+        const sourcePath = path.join(sourceBase, 'agents', fileName);
+        const targetPath = path.join(agentsDir, fileName);
+
+        if (await fs.pathExists(sourcePath)) {
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
+        }
+      }
+    }
+
+    if (files.tasks && files.tasks.length > 0) {
+      const tasksDir = path.join(targetBase, 'tasks');
+      await fs.ensureDir(tasksDir);
+
+      for (const taskPath of files.tasks) {
+        const fileName = path.basename(taskPath);
+        const sourcePath = path.join(sourceBase, 'tasks', fileName);
+        const targetPath = path.join(tasksDir, fileName);
+
+        if (await fs.pathExists(sourcePath)) {
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
+        }
+      }
+    }
+
+    if (files.tools && files.tools.length > 0) {
+      const toolsDir = path.join(targetBase, 'tools');
+      await fs.ensureDir(toolsDir);
+
+      for (const toolPath of files.tools) {
+        const fileName = path.basename(toolPath);
+        const sourcePath = path.join(sourceBase, 'tools', fileName);
+        const targetPath = path.join(toolsDir, fileName);
+
+        if (await fs.pathExists(sourcePath)) {
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
+        }
+      }
+    }
+
+    if (files.templates && files.templates.length > 0) {
+      const templatesDir = path.join(targetBase, 'templates');
+      await fs.ensureDir(templatesDir);
+
+      for (const templatePath of files.templates) {
+        const fileName = path.basename(templatePath);
+        const sourcePath = path.join(sourceBase, 'templates', fileName);
+        const targetPath = path.join(templatesDir, fileName);
+
+        if (await fs.pathExists(sourcePath)) {
+          await this.copyFileWithPlaceholderReplacement(sourcePath, targetPath);
+          this.installedFiles.add(targetPath);
+        }
+      }
+    }
+
+    if (files.data && files.data.length > 0) {
+      for (const dataPath of files.data) {
+        // Preserve directory structure for data files
+        const relative = path.relative(sourceBase, dataPath);
+        const targetPath = path.join(targetBase, relative);
+
+        await fs.ensureDir(path.dirname(targetPath));
+
+        if (await fs.pathExists(dataPath)) {
+          await this.copyFileWithPlaceholderReplacement(dataPath, targetPath);
+          this.installedFiles.add(targetPath);
+        }
+      }
+    }
+
+    // Create a marker file to indicate this is a partial installation
+    const markerPath = path.join(targetBase, '.partial');
+    await fs.writeFile(
+      markerPath,
+      `This module contains only dependencies required by other modules.\nInstalled: ${new Date().toISOString()}\n`,
+    );
+  }
+
+  /**
+   * Private: Install core
+   * @param {string} bmadDir - BMAD installation directory
+   */
+  async installCore(bmadDir) {
+    const sourcePath = getModulePath('core');
+    const targetPath = path.join(bmadDir, 'core');
+
+    // 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 core files (similar to copyModuleWithFiltering but for core)
+   * @param {string} sourcePath - Source path
+   * @param {string} targetPath - Target path
+   */
+  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') || file === 'custom.yaml' || file.endsWith('/custom.yaml')) {
+        continue;
+      }
+
+      // Skip .agent.yaml files - they will be compiled separately
+      if (file.endsWith('.agent.yaml')) {
+        continue;
+      }
+
+      const sourceFile = path.join(sourcePath, file);
+      const targetFile = path.join(targetPath, file);
+
+      // Check if this is an agent file
+      if (file.startsWith('agents/') && file.endsWith('.md')) {
+        // Read the file to check for localskip
+        const content = await fs.readFile(sourceFile, 'utf8');
+
+        // Check for localskip="true" in the agent tag
+        const agentMatch = content.match(/<agent[^>]*\slocalskip="true"[^>]*>/);
+        if (agentMatch) {
+          console.log(chalk.dim(`  Skipping web-only agent: ${path.basename(file)}`));
+          continue; // Skip this agent
+        }
+      }
+
+      // Copy the file with placeholder replacement
+      await fs.ensureDir(path.dirname(targetFile));
+      await this.copyFileWithPlaceholderReplacement(sourceFile, targetFile);
+
+      // Track the installed file
+      this.installedFiles.add(targetFile);
+    }
+  }
+
+  /**
+   * Get list of all files in a directory recursively
+   * @param {string} dir - Directory path
+   * @param {string} baseDir - Base directory for relative paths
+   * @returns {Array} List of relative file paths
+   */
+  async getFileList(dir, baseDir = dir) {
+    const files = [];
+    const entries = await fs.readdir(dir, { withFileTypes: true });
+
+    for (const entry of entries) {
+      const fullPath = path.join(dir, entry.name);
+
+      if (entry.isDirectory()) {
+        // Skip _module-installer directories
+        if (entry.name === '_module-installer') {
+          continue;
+        }
+        const subFiles = await this.getFileList(fullPath, baseDir);
+        files.push(...subFiles);
+      } else {
+        files.push(path.relative(baseDir, fullPath));
+      }
+    }
+
+    return files;
+  }
+
+  /**
+   * Process agent files to build YAML agents and inject activation blocks
+   * @param {string} modulePath - Path to module in bmad/ installation
+   * @param {string} moduleName - Module name
+   */
+  async processAgentFiles(modulePath, moduleName) {
+    const agentsPath = path.join(modulePath, 'agents');
+
+    // Check if agents directory exists
+    if (!(await fs.pathExists(agentsPath))) {
+      return; // No agents to process
+    }
+
+    // Determine project directory (parent of bmad/ directory)
+    const bmadDir = path.dirname(modulePath);
+    const cfgAgentsDir = path.join(bmadDir, '_config', 'agents');
+
+    // Ensure _config/agents directory exists
+    await fs.ensureDir(cfgAgentsDir);
+
+    // Get all agent files
+    const agentFiles = await fs.readdir(agentsPath);
+
+    for (const agentFile of agentFiles) {
+      // Skip .agent.yaml files - they should already be compiled by compileModuleAgents
+      if (agentFile.endsWith('.agent.yaml')) {
+        continue;
+      }
+
+      // Only process .md files (already compiled from YAML)
+      if (!agentFile.endsWith('.md')) {
+        continue;
+      }
+
+      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`));
+          }
+        }
+      }
+    }
+  }
+
+  /**
+   * Private: Update core
+   */
+  async updateCore(bmadDir, force = false) {
+    const sourcePath = getModulePath('core');
+    const targetPath = path.join(bmadDir, 'core');
+
+    if (force) {
+      await fs.remove(targetPath);
+      await this.installCore(bmadDir);
+    } 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');
+    }
+  }
+
+  /**
+   * Quick update method - preserves all settings and only prompts for new config fields
+   * @param {Object} config - Configuration with directory
+   * @returns {Object} Update result
+   */
+  async quickUpdate(config) {
+    const ora = require('ora');
+    const spinner = ora('Starting quick update...').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.`);
+      }
+
+      spinner.text = 'Detecting installed modules and configuration...';
+
+      // Detect existing installation
+      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;
+            }
+
+            // Check if this is an external official module - skip cache for those
+            const isExternal = await this.moduleManager.isExternalModule(moduleId);
+            if (isExternal) {
+              // External modules are handled via cloneExternalModule, not from cache
+              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 availableModulesData = await this.moduleManager.listAvailable();
+      const availableModules = [...availableModulesData.modules, ...availableModulesData.customModules];
+
+      // Add external official modules to available modules
+      // These can always be obtained by cloning from their remote URLs
+      const { ExternalModuleManager } = require('../modules/external-manager');
+      const externalManager = new ExternalModuleManager();
+      const externalModules = await externalManager.listAvailable();
+      for (const externalModule of externalModules) {
+        // Only add if not already in the list and is installed
+        if (installedModules.includes(externalModule.code) && !availableModules.some((m) => m.id === externalModule.code)) {
+          availableModules.push({
+            id: externalModule.code,
+            name: externalModule.name,
+            isExternal: true,
+            fromExternal: true,
+          });
+        }
+      }
+
+      // 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 = 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)`);
+
+      if (skippedModules.length > 0) {
+        console.log(chalk.yellow(`⚠️  Skipping ${skippedModules.length} module(s) - no source available: ${skippedModules.join(', ')}`));
+      }
+
+      // Load existing configs and collect new fields (if any)
+      console.log(chalk.cyan('\n📋 Checking for new configuration options...'));
+      await this.configCollector.loadExistingConfig(projectDir);
+
+      let promptedForNewFields = false;
+
+      // Check core config for new fields
+      const corePrompted = await this.configCollector.collectModuleConfigQuick('core', projectDir, true);
+      if (corePrompted) {
+        promptedForNewFields = true;
+      }
+
+      // Check each module we're updating for new fields (NOT skipped modules)
+      for (const moduleName of modulesToUpdate) {
+        const modulePrompted = await this.configCollector.collectModuleConfigQuick(moduleName, projectDir, true);
+        if (modulePrompted) {
+          promptedForNewFields = true;
+        }
+      }
+
+      if (!promptedForNewFields) {
+        console.log(chalk.green('✓ All configuration is up to date, no new options to configure'));
+      }
+
+      // Add metadata
+      this.configCollector.collectedConfig._meta = {
+        version: require(path.join(getProjectRoot(), 'package.json')).version,
+        installDate: new Date().toISOString(),
+        lastModified: new Date().toISOString(),
+      };
+
+      // Build the config object for the installer
+      const installConfig = {
+        directory: projectDir,
+        installCore: true,
+        modules: modulesToUpdate, // Only update modules we have source for
+        ides: configuredIdes,
+        skipIde: configuredIdes.length === 0,
+        coreConfig: this.configCollector.collectedConfig.core,
+        actionType: 'install', // Use regular install flow
+        _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);
+
+      // 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,
+        moduleCount: modulesToUpdate.length + 1, // +1 for core
+        hadNewFields: promptedForNewFields,
+        modules: ['core', ...modulesToUpdate],
+        skippedModules: skippedModules,
+        ides: configuredIdes,
+      };
+    } catch (error) {
+      spinner.fail('Quick update failed');
+      throw error;
+    }
+  }
+
+  /**
+   * 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)) {
+              // Check if this is an external official module - skip cache for those
+              const isExternal = await this.moduleManager.isExternalModule(moduleId);
+              if (isExternal) {
+                // External modules are handled via cloneExternalModule, not from cache
+                continue;
+              }
+              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
+   */
+  async promptUpdateAction() {
+    const action = await prompts.select({
+      message: 'What would you like to do?',
+      choices: [{ name: 'Update existing installation', value: 'update' }],
+    });
+    return { action };
+  }
+
+  /**
+   * Handle legacy BMAD v4 detection with simple warning
+   * @param {string} _projectDir - Project directory (unused in simplified version)
+   * @param {Object} _legacyV4 - Legacy V4 detection result (unused in simplified version)
+   */
+  async handleLegacyV4Migration(_projectDir, _legacyV4) {
+    console.log('');
+    console.log(chalk.yellow.bold('⚠️  Legacy BMAD v4 detected'));
+    console.log(chalk.yellow('─'.repeat(80)));
+    console.log(chalk.yellow('Found .bmad-method folder from BMAD v4 installation.'));
+    console.log('');
+
+    console.log(chalk.dim('Before continuing with installation, we recommend:'));
+    console.log(chalk.dim('  1. Remove the .bmad-method folder, OR'));
+    console.log(chalk.dim('  2. Back it up by renaming it to another name (e.g., bmad-method-backup)'));
+    console.log('');
+
+    console.log(chalk.dim('If your v4 installation set up rules or commands, you should remove those as well.'));
+    console.log('');
+
+    const proceed = await prompts.select({
+      message: 'What would you like to do?',
+      choices: [
+        {
+          name: 'Exit and clean up manually (recommended)',
+          value: 'exit',
+          hint: 'Exit installation',
+        },
+        {
+          name: 'Continue with installation anyway',
+          value: 'continue',
+          hint: 'Continue',
+        },
+      ],
+      default: 'exit',
+    });
+
+    if (proceed === 'exit') {
+      console.log('');
+      console.log(chalk.cyan('Please remove the .bmad-method folder and any v4 rules/commands,'));
+      console.log(chalk.cyan('then run the installer again.'));
+      console.log('');
+      process.exit(0);
+    }
+
+    console.log('');
+    console.log(chalk.yellow('⚠️  Proceeding with installation despite legacy v4 folder'));
+    console.log('');
+  }
+
+  /**
+   * Read files-manifest.csv
+   * @param {string} bmadDir - BMAD installation directory
+   * @returns {Array} Array of file entries from files-manifest.csv
+   */
+  async readFilesManifest(bmadDir) {
+    const filesManifestPath = path.join(bmadDir, '_config', 'files-manifest.csv');
+    if (!(await fs.pathExists(filesManifestPath))) {
+      return [];
+    }
+
+    try {
+      const content = await fs.readFile(filesManifestPath, 'utf8');
+      const lines = content.split('\n');
+      const files = [];
+
+      for (let i = 1; i < lines.length; i++) {
+        // Skip header
+        const line = lines[i].trim();
+        if (!line) continue;
+
+        // Parse CSV line properly handling quoted values
+        const parts = [];
+        let current = '';
+        let inQuotes = false;
+
+        for (const char of line) {
+          if (char === '"') {
+            inQuotes = !inQuotes;
+          } else if (char === ',' && !inQuotes) {
+            parts.push(current);
+            current = '';
+          } else {
+            current += char;
+          }
+        }
+        parts.push(current); // Add last part
+
+        if (parts.length >= 4) {
+          files.push({
+            type: parts[0],
+            name: parts[1],
+            module: parts[2],
+            path: parts[3],
+            hash: parts[4] || null, // Hash may not exist in old manifests
+          });
+        }
+      }
+
+      return files;
+    } catch (error) {
+      console.warn('Warning: Could not read files-manifest.csv:', error.message);
+      return [];
+    }
+  }
+
+  /**
+   * Detect custom and modified files
+   * @param {string} bmadDir - BMAD installation directory
+   * @param {Array} existingFilesManifest - Previous files from files-manifest.csv
+   * @returns {Object} Object with customFiles and modifiedFiles arrays
+   */
+  async detectCustomFiles(bmadDir, existingFilesManifest) {
+    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) {
+      manifestHasHashes = existingFilesManifest.some((f) => f.hash);
+    }
+
+    // Build map of previously installed files from files-manifest.csv with their hashes
+    const installedFilesMap = new Map();
+    for (const fileEntry of existingFilesManifest) {
+      if (fileEntry.path) {
+        const absolutePath = path.join(bmadDir, fileEntry.path);
+        installedFilesMap.set(path.normalize(absolutePath), {
+          hash: fileEntry.hash,
+          relativePath: fileEntry.path,
+        });
+      }
+    }
+
+    // Recursively scan bmadDir for all files
+    const scanDirectory = async (dir) => {
+      try {
+        const entries = await fs.readdir(dir, { withFileTypes: true });
+        for (const entry of entries) {
+          const fullPath = path.join(dir, entry.name);
+
+          if (entry.isDirectory()) {
+            // Skip certain directories
+            if (entry.name === 'node_modules' || entry.name === '.git') {
+              continue;
+            }
+            await scanDirectory(fullPath);
+          } else if (entry.isFile()) {
+            const normalizedPath = path.normalize(fullPath);
+            const fileInfo = installedFilesMap.get(normalizedPath);
+
+            // Skip certain system files that are auto-generated
+            const relativePath = path.relative(bmadDir, fullPath);
+            const fileName = path.basename(fullPath);
+
+            // 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
+            if (fileName === 'config.yaml') {
+              continue;
+            }
+
+            if (!fileInfo) {
+              // File not in manifest = custom file
+              // 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);
+              if (currentHash && currentHash !== fileInfo.hash) {
+                // Hash changed = file was modified
+                modifiedFiles.push({
+                  path: fullPath,
+                  relativePath: fileInfo.relativePath,
+                });
+              }
+            }
+          }
+        }
+      } catch {
+        // Ignore errors scanning directories
+      }
+    };
+
+    await scanDirectory(bmadDir);
+    return { customFiles, modifiedFiles };
+  }
+
+  /**
+   * 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 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,
+          });
+        }
+      }
+    }
+
+    // If no missing sources, return immediately
+    if (customModulesWithMissingSources.length === 0) {
+      return {
+        validCustomModules,
+        keptModulesWithoutSources: [],
+      };
+    }
+
+    // Stop any spinner for interactive prompts
+    const currentSpinner = ora();
+    if (currentSpinner.isSpinning) {
+      currentSpinner.stop();
+    }
+
+    console.log(chalk.yellow(`\n⚠️  Found ${customModulesWithMissingSources.length} custom module(s) with missing sources:`));
+
+    let keptCount = 0;
+    let updatedCount = 0;
+    let removedCount = 0;
+
+    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: ${missing.sourcePath}`));
+
+      const choices = [
+        {
+          name: 'Keep installed (will not be processed)',
+          value: 'keep',
+          hint: 'Keep',
+        },
+        {
+          name: 'Specify new source location',
+          value: 'update',
+          hint: 'Update',
+        },
+      ];
+
+      // Only add remove option if not just compiling agents
+      if (operation !== 'compile-agents') {
+        choices.push({
+          name: '⚠️  REMOVE module completely (destructive!)',
+          value: 'remove',
+          hint: 'Remove',
+        });
+      }
+
+      const action = await prompts.select({
+        message: `How would you like to handle "${missing.name}"?`,
+        choices,
+      });
+
+      switch (action) {
+        case 'update': {
+          // Use sync validation because @clack/prompts doesn't support async validate
+          const newSourcePath = await prompts.text({
+            message: 'Enter the new path to the custom module:',
+            default: missing.sourcePath,
+            validate: (input) => {
+              if (!input || input.trim() === '') {
+                return 'Please enter a path';
+              }
+              const expandedPath = path.resolve(input.trim());
+              if (!fs.pathExistsSync(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 (!fs.pathExistsSync(moduleYamlPath) && !fs.pathExistsSync(agentsPath) && !fs.pathExistsSync(workflowsPath)) {
+                return 'Path does not appear to contain a valid custom module';
+              }
+              return; // clack expects undefined for valid input
+            },
+          });
+
+          // 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,
+          });
+
+          updatedCount++;
+          console.log(chalk.green(`✓ Updated source location`));
+
+          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)}`));
+
+          const confirmDelete = await prompts.confirm({
+            message: chalk.red.bold('Are you absolutely sure you want to delete this module?'),
+            default: false,
+          });
+
+          if (confirmDelete) {
+            const typedConfirm = await prompts.text({
+              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; // clack expects undefined for valid input
+              },
+            });
+
+            if (typedConfirm === 'DELETE') {
+              // Remove the module from filesystem and manifest
+              const modulePath = path.join(bmadDir, missing.id);
+              if (await fs.pathExists(modulePath)) {
+                const fsExtra = require('fs-extra');
+                await fsExtra.remove(modulePath);
+                console.log(chalk.yellow(`  ✓ Deleted module directory: ${path.relative(projectRoot, modulePath)}`));
+              }
+
+              await this.manifest.removeModule(bmadDir, missing.id);
+              await this.manifest.removeCustomModule(bmadDir, missing.id);
+              console.log(chalk.yellow(`  ✓ Removed from manifest`));
+
+              // Also remove from installedModules list
+              if (installedModules && installedModules.includes(missing.id)) {
+                const index = installedModules.indexOf(missing.id);
+                if (index !== -1) {
+                  installedModules.splice(index, 1);
+                }
+              }
+
+              removedCount++;
+              console.log(chalk.red.bold(`✓ "${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++;
+          }
+
+          break;
+        }
+        case 'keep': {
+          keptCount++;
+          keptModulesWithoutSources.push(missing.id);
+          console.log(chalk.dim(`  Module will be kept as-is`));
+
+          break;
+        }
+        // No default
+      }
+    }
+
+    // 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,
+    };
+  }
+}
+
+module.exports = { Installer };