scm-method 1.0.0

package/tools/installer/core/installer.js

@@ -0,0 +1,1790 @@
+const path = require('node:path');
+const fs = require('fs-extra');
+const { Manifest } = require('./manifest');
+const { OfficialModules } = require('../modules/official-modules');
+const { CustomModules } = require('../modules/custom-modules');
+const { IdeManager } = require('../ide/manager');
+const { FileOps } = require('../file-ops');
+const { Config } = require('./config');
+const { getProjectRoot, getSourcePath } = require('../project-root');
+const { ManifestGenerator } = require('./manifest-generator');
+const prompts = require('../prompts');
+const { SCM_FOLDER_NAME } = require('../ide/shared/path-utils');
+const { InstallPaths } = require('./install-paths');
+const { ExternalModuleManager } = require('../modules/external-manager');
+
+const { ExistingInstall } = require('./existing-install');
+
+class Installer {
+  constructor() {
+    this.externalModuleManager = new ExternalModuleManager();
+    this.manifest = new Manifest();
+    this.customModules = new CustomModules();
+    this.ideManager = new IdeManager();
+    this.fileOps = new FileOps();
+    this.installedFiles = new Set(); // Track all installed files
+    this.scmFolderName = SCM_FOLDER_NAME;
+  }
+
+  /**
+   * Main installation method
+   * @param {Object} config - Installation configuration
+   * @param {string} config.directory - Target directory
+   * @param {string[]} config.modules - Modules to install (including 'core')
+   * @param {string[]} config.ides - IDEs to configure
+   */
+  async install(originalConfig) {
+    let updateState = null;
+
+    try {
+      const config = Config.build(originalConfig);
+      const paths = await InstallPaths.create(config);
+      const officialModules = await OfficialModules.build(config, paths);
+      const existingInstall = await ExistingInstall.detect(paths.scmDir);
+
+      await this.customModules.discoverPaths(originalConfig, paths);
+
+      if (existingInstall.installed) {
+        await this._removeDeselectedModules(existingInstall, config, paths);
+        updateState = await this._prepareUpdateState(paths, config, existingInstall, officialModules);
+        await this._removeDeselectedIdes(existingInstall, config, paths);
+      }
+
+      await this._validateIdeSelection(config);
+
+      // Results collector for consolidated summary
+      const results = [];
+      const addResult = (step, status, detail = '') => results.push({ step, status, detail });
+
+      await this._cacheCustomModules(paths, addResult);
+
+      // Compute module lists: official = selected minus custom, all = both
+      const customModuleIds = new Set(this.customModules.paths.keys());
+      const officialModuleIds = (config.modules || []).filter((m) => !customModuleIds.has(m));
+      const allModules = [...officialModuleIds, ...[...customModuleIds].filter((id) => !officialModuleIds.includes(id))];
+
+      await this._installAndConfigure(config, originalConfig, paths, officialModuleIds, allModules, addResult, officialModules);
+
+      await this._setupIdes(config, allModules, paths, addResult);
+
+      const restoreResult = await this._restoreUserFiles(paths, updateState);
+
+      // Render consolidated summary
+      await this.renderInstallSummary(results, {
+        scmDir: paths.scmDir,
+        modules: config.modules,
+        ides: config.ides,
+        customFiles: restoreResult.customFiles.length > 0 ? restoreResult.customFiles : undefined,
+        modifiedFiles: restoreResult.modifiedFiles.length > 0 ? restoreResult.modifiedFiles : undefined,
+      });
+
+      return {
+        success: true,
+        path: paths.scmDir,
+        modules: config.modules,
+        ides: config.ides,
+        projectDir: paths.projectRoot,
+      };
+    } catch (error) {
+      await prompts.log.error('Installation failed');
+
+      // Clean up any temp backup directories that were created before the failure
+      try {
+        if (updateState?.tempBackupDir && (await fs.pathExists(updateState.tempBackupDir))) {
+          await fs.remove(updateState.tempBackupDir);
+        }
+        if (updateState?.tempModifiedBackupDir && (await fs.pathExists(updateState.tempModifiedBackupDir))) {
+          await fs.remove(updateState.tempModifiedBackupDir);
+        }
+      } catch {
+        // Best-effort cleanup — don't mask the original error
+      }
+
+      throw error;
+    }
+  }
+
+  /**
+   * Remove modules that were previously installed but are no longer selected.
+   * No confirmation — the user's module selection is the decision.
+   */
+  async _removeDeselectedModules(existingInstall, config, paths) {
+    const previouslyInstalled = new Set(existingInstall.moduleIds);
+    const newlySelected = new Set(config.modules || []);
+    const toRemove = [...previouslyInstalled].filter((m) => !newlySelected.has(m) && m !== 'core');
+
+    for (const moduleId of toRemove) {
+      const modulePath = paths.moduleDir(moduleId);
+      try {
+        if (await fs.pathExists(modulePath)) {
+          await fs.remove(modulePath);
+        }
+      } catch (error) {
+        await prompts.log.warn(`Warning: Failed to remove ${moduleId}: ${error.message}`);
+      }
+    }
+  }
+
+  /**
+   * Fail fast if all selected IDEs are suspended.
+   */
+  async _validateIdeSelection(config) {
+    if (!config.ides || config.ides.length === 0) return;
+
+    await this.ideManager.ensureInitialized();
+    const suspendedIdes = config.ides.filter((ide) => {
+      const handler = this.ideManager.handlers.get(ide);
+      return handler?.platformConfig?.suspended;
+    });
+
+    if (suspendedIdes.length > 0 && suspendedIdes.length === config.ides.length) {
+      for (const ide of suspendedIdes) {
+        const handler = this.ideManager.handlers.get(ide);
+        await prompts.log.error(`${handler.displayName || ide}: ${handler.platformConfig.suspended}`);
+      }
+      throw new Error(
+        `All selected tool(s) are suspended: ${suspendedIdes.join(', ')}. Installation aborted to prevent upgrading _scm/ without a working IDE configuration.`,
+      );
+    }
+  }
+
+  /**
+   * Remove IDEs that were previously installed but are no longer selected.
+   * No confirmation — the user's IDE selection is the decision.
+   */
+  async _removeDeselectedIdes(existingInstall, config, paths) {
+    const previouslyInstalled = new Set(existingInstall.ides);
+    const newlySelected = new Set(config.ides || []);
+    const toRemove = [...previouslyInstalled].filter((ide) => !newlySelected.has(ide));
+
+    if (toRemove.length === 0) return;
+
+    await this.ideManager.ensureInitialized();
+    for (const ide of toRemove) {
+      try {
+        const handler = this.ideManager.handlers.get(ide);
+        if (handler) {
+          await handler.cleanup(paths.projectRoot);
+        }
+      } catch (error) {
+        await prompts.log.warn(`Warning: Failed to remove ${ide}: ${error.message}`);
+      }
+    }
+  }
+
+  /**
+   * Cache custom modules into the local cache directory.
+   * Updates this.customModules.paths in place with cached locations.
+   */
+  async _cacheCustomModules(paths, addResult) {
+    if (!this.customModules.paths || this.customModules.paths.size === 0) return;
+
+    const { CustomModuleCache } = require('./custom-module-cache');
+    const customCache = new CustomModuleCache(paths.scmDir);
+
+    for (const [moduleId, sourcePath] of this.customModules.paths) {
+      const cachedInfo = await customCache.cacheModule(moduleId, sourcePath, {
+        sourcePath: sourcePath,
+      });
+      this.customModules.paths.set(moduleId, cachedInfo.cachePath);
+    }
+
+    addResult('Custom modules cached', 'ok');
+  }
+
+  /**
+   * Install modules, create directories, generate configs and manifests.
+   */
+  async _installAndConfigure(config, originalConfig, paths, officialModuleIds, allModules, addResult, officialModules) {
+    const isQuickUpdate = config.isQuickUpdate();
+    const moduleConfigs = officialModules.moduleConfigs;
+
+    const dirResults = { createdDirs: [], movedDirs: [], createdWdsFolders: [] };
+
+    const installTasks = [];
+
+    if (allModules.length > 0) {
+      installTasks.push({
+        title: isQuickUpdate ? `Updating ${allModules.length} module(s)` : `Installing ${allModules.length} module(s)`,
+        task: async (message) => {
+          const installedModuleNames = new Set();
+
+          await this._installOfficialModules(config, paths, officialModuleIds, addResult, isQuickUpdate, officialModules, {
+            message,
+            installedModuleNames,
+          });
+
+          await this._installCustomModules(config, paths, addResult, officialModules, {
+            message,
+            installedModuleNames,
+          });
+
+          return `${allModules.length} module(s) ${isQuickUpdate ? 'updated' : 'installed'}`;
+        },
+      });
+    }
+
+    installTasks.push({
+      title: 'Creating module directories',
+      task: async (message) => {
+        const verboseMode = process.env.SCM_VERBOSE_INSTALL === 'true' || config.verbose;
+        const moduleLogger = {
+          log: async (msg) => (verboseMode ? await prompts.log.message(msg) : undefined),
+          error: async (msg) => await prompts.log.error(msg),
+          warn: async (msg) => await prompts.log.warn(msg),
+        };
+
+        if (config.modules && config.modules.length > 0) {
+          for (const moduleName of config.modules) {
+            message(`Setting up ${moduleName}...`);
+            const result = await officialModules.createModuleDirectories(moduleName, paths.scmDir, {
+              installedIDEs: config.ides || [],
+              moduleConfig: moduleConfigs[moduleName] || {},
+              existingModuleConfig: officialModules.existingConfig?.[moduleName] || {},
+              coreConfig: moduleConfigs.core || {},
+              logger: moduleLogger,
+              silent: true,
+            });
+            if (result) {
+              dirResults.createdDirs.push(...result.createdDirs);
+              dirResults.movedDirs.push(...(result.movedDirs || []));
+              dirResults.createdWdsFolders.push(...result.createdWdsFolders);
+            }
+          }
+        }
+
+        addResult('Module directories', 'ok');
+        return 'Module directories created';
+      },
+    });
+
+    const configTask = {
+      title: 'Generating configurations',
+      task: async (message) => {
+        await this.generateModuleConfigs(paths.scmDir, moduleConfigs);
+        addResult('Configurations', 'ok', 'generated');
+
+        this.installedFiles.add(paths.manifestFile());
+        this.installedFiles.add(paths.agentManifest());
+
+        message('Generating manifests...');
+        const manifestGen = new ManifestGenerator();
+
+        const allModulesForManifest = config.isQuickUpdate()
+          ? originalConfig._existingModules || allModules || []
+          : originalConfig._preserveModules
+            ? [...allModules, ...originalConfig._preserveModules]
+            : allModules || [];
+
+        let modulesForCsvPreserve;
+        if (config.isQuickUpdate()) {
+          modulesForCsvPreserve = originalConfig._existingModules || allModules || [];
+        } else {
+          modulesForCsvPreserve = originalConfig._preserveModules ? [...allModules, ...originalConfig._preserveModules] : allModules;
+        }
+
+        await manifestGen.generateManifests(paths.scmDir, allModulesForManifest, [...this.installedFiles], {
+          ides: config.ides || [],
+          preservedModules: modulesForCsvPreserve,
+        });
+
+        message('Generating help catalog...');
+        await this.mergeModuleHelpCatalogs(paths.scmDir);
+        addResult('Help catalog', 'ok');
+
+        return 'Configurations generated';
+      },
+    };
+    installTasks.push(configTask);
+
+    // Run install + dirs first, then render dir output, then run config generation
+    const mainTasks = installTasks.filter((t) => t !== configTask);
+    await prompts.tasks(mainTasks);
+
+    const color = await prompts.getColor();
+    if (dirResults.movedDirs.length > 0) {
+      const lines = dirResults.movedDirs.map((d) => `  ${d}`).join('\n');
+      await prompts.log.message(color.cyan(`Moved directories:\n${lines}`));
+    }
+    if (dirResults.createdDirs.length > 0) {
+      const lines = dirResults.createdDirs.map((d) => `  ${d}`).join('\n');
+      await prompts.log.message(color.yellow(`Created directories:\n${lines}`));
+    }
+    if (dirResults.createdWdsFolders.length > 0) {
+      const lines = dirResults.createdWdsFolders.map((f) => color.dim(`  \u2713 ${f}/`)).join('\n');
+      await prompts.log.message(color.cyan(`Created WDS folder structure:\n${lines}`));
+    }
+
+    await prompts.tasks([configTask]);
+  }
+
+  /**
+   * Set up IDE integrations for each selected IDE.
+   */
+  async _setupIdes(config, allModules, paths, addResult) {
+    if (config.skipIde || !config.ides || config.ides.length === 0) return;
+
+    await this.ideManager.ensureInitialized();
+    const validIdes = config.ides.filter((ide) => ide && typeof ide === 'string');
+
+    if (validIdes.length === 0) {
+      addResult('IDE configuration', 'warn', 'no valid IDEs selected');
+      return;
+    }
+
+    for (const ide of validIdes) {
+      const setupResult = await this.ideManager.setup(ide, paths.projectRoot, paths.scmDir, {
+        selectedModules: allModules || [],
+        verbose: config.verbose,
+      });
+
+      if (setupResult.success) {
+        addResult(ide, 'ok', setupResult.detail || '');
+      } else {
+        addResult(ide, 'error', setupResult.error || 'failed');
+      }
+    }
+  }
+
+  /**
+   * Restore custom and modified files that were backed up before the update.
+   * No-op for fresh installs (updateState is null).
+   * @param {Object} paths - InstallPaths instance
+   * @param {Object|null} updateState - From _prepareUpdateState, or null for fresh installs
+   * @returns {Object} { customFiles, modifiedFiles } — lists of restored files
+   */
+  async _restoreUserFiles(paths, updateState) {
+    const noFiles = { customFiles: [], modifiedFiles: [] };
+
+    if (!updateState || (updateState.customFiles.length === 0 && updateState.modifiedFiles.length === 0)) {
+      return noFiles;
+    }
+
+    let restoredCustomFiles = [];
+    let restoredModifiedFiles = [];
+
+    await prompts.tasks([
+      {
+        title: 'Finalizing installation',
+        task: async (message) => {
+          if (updateState.customFiles.length > 0) {
+            message(`Restoring ${updateState.customFiles.length} custom files...`);
+
+            for (const originalPath of updateState.customFiles) {
+              const relativePath = path.relative(paths.scmDir, originalPath);
+              const backupPath = path.join(updateState.tempBackupDir, relativePath);
+
+              if (await fs.pathExists(backupPath)) {
+                await fs.ensureDir(path.dirname(originalPath));
+                await fs.copy(backupPath, originalPath, { overwrite: true });
+              }
+            }
+
+            if (updateState.tempBackupDir && (await fs.pathExists(updateState.tempBackupDir))) {
+              await fs.remove(updateState.tempBackupDir);
+            }
+
+            restoredCustomFiles = updateState.customFiles;
+          }
+
+          if (updateState.modifiedFiles.length > 0) {
+            restoredModifiedFiles = updateState.modifiedFiles;
+
+            if (updateState.tempModifiedBackupDir && (await fs.pathExists(updateState.tempModifiedBackupDir))) {
+              message(`Restoring ${restoredModifiedFiles.length} modified files as .bak...`);
+
+              for (const modifiedFile of restoredModifiedFiles) {
+                const relativePath = path.relative(paths.scmDir, modifiedFile.path);
+                const tempBackupPath = path.join(updateState.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 });
+                }
+              }
+
+              await fs.remove(updateState.tempModifiedBackupDir);
+            }
+          }
+
+          return 'Installation finalized';
+        },
+      },
+    ]);
+
+    return { customFiles: restoredCustomFiles, modifiedFiles: restoredModifiedFiles };
+  }
+
+  /**
+   * Scan the custom module cache directory and register any cached custom modules
+   * that aren't already known from the manifest or external module list.
+   * @param {Object} paths - InstallPaths instance
+   */
+  async _scanCachedCustomModules(paths) {
+    const cacheDir = paths.customCacheDir;
+    if (!(await fs.pathExists(cacheDir))) {
+      return;
+    }
+
+    const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
+
+    for (const cachedModule of cachedModules) {
+      const moduleId = cachedModule.name;
+      const cachedPath = path.join(cacheDir, moduleId);
+
+      // Skip if path doesn't exist (broken symlink, deleted dir) - avoids lstat ENOENT
+      if (!(await fs.pathExists(cachedPath)) || !cachedModule.isDirectory()) {
+        continue;
+      }
+
+      // Skip if we already have this module from manifest
+      if (this.customModules.paths.has(moduleId)) {
+        continue;
+      }
+
+      // Check if this is an external official module - skip cache for those
+      const isExternal = await this.externalModuleManager.hasModule(moduleId);
+      if (isExternal) {
+        continue;
+      }
+
+      // Check if this is actually a custom module (has module.yaml)
+      const moduleYamlPath = path.join(cachedPath, 'module.yaml');
+      if (await fs.pathExists(moduleYamlPath)) {
+        this.customModules.paths.set(moduleId, cachedPath);
+      }
+    }
+  }
+
+  /**
+   * Common update preparation: detect files, preserve core config, scan cache, back up.
+   * @param {Object} paths - InstallPaths instance
+   * @param {Object} config - Clean config (may have coreConfig updated)
+   * @param {Object} existingInstall - Detection result
+   * @param {Object} officialModules - OfficialModules instance
+   * @returns {Object} Update state: { customFiles, modifiedFiles, tempBackupDir, tempModifiedBackupDir }
+   */
+  async _prepareUpdateState(paths, config, existingInstall, officialModules) {
+    // Detect custom and modified files BEFORE updating (compare current files vs files-manifest.csv)
+    const existingFilesManifest = await this.readFilesManifest(paths.scmDir);
+    const { customFiles, modifiedFiles } = await this.detectCustomFiles(paths.scmDir, existingFilesManifest);
+
+    // Preserve existing core configuration during updates
+    // (no-op for quick-update which already has core config from collectModuleConfigQuick)
+    const coreConfigPath = paths.moduleConfig('core');
+    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);
+
+        config.coreConfig = existingCoreConfig;
+        officialModules.moduleConfigs.core = existingCoreConfig;
+      } catch (error) {
+        await prompts.log.warn(`Warning: Could not read existing core config: ${error.message}`);
+      }
+    }
+
+    await this._scanCachedCustomModules(paths);
+
+    const backupDirs = await this._backupUserFiles(paths, customFiles, modifiedFiles);
+
+    return {
+      customFiles,
+      modifiedFiles,
+      tempBackupDir: backupDirs.tempBackupDir,
+      tempModifiedBackupDir: backupDirs.tempModifiedBackupDir,
+    };
+  }
+
+  /**
+   * Back up custom and modified files to temp directories before overwriting.
+   * Returns the temp directory paths (or undefined if no files to back up).
+   * @param {Object} paths - InstallPaths instance
+   * @param {string[]} customFiles - Absolute paths of custom (user-added) files
+   * @param {Object[]} modifiedFiles - Array of { path, relativePath } for modified files
+   * @returns {Object} { tempBackupDir, tempModifiedBackupDir } — undefined if no files
+   */
+  async _backupUserFiles(paths, customFiles, modifiedFiles) {
+    let tempBackupDir;
+    let tempModifiedBackupDir;
+
+    if (customFiles.length > 0) {
+      tempBackupDir = path.join(paths.projectRoot, '_scm-custom-backup-temp');
+      await fs.ensureDir(tempBackupDir);
+
+      for (const customFile of customFiles) {
+        const relativePath = path.relative(paths.scmDir, customFile);
+        const backupPath = path.join(tempBackupDir, relativePath);
+        await fs.ensureDir(path.dirname(backupPath));
+        await fs.copy(customFile, backupPath);
+      }
+    }
+
+    if (modifiedFiles.length > 0) {
+      tempModifiedBackupDir = path.join(paths.projectRoot, '_scm-modified-backup-temp');
+      await fs.ensureDir(tempModifiedBackupDir);
+
+      for (const modifiedFile of modifiedFiles) {
+        const relativePath = path.relative(paths.scmDir, modifiedFile.path);
+        const tempBackupPath = path.join(tempModifiedBackupDir, relativePath);
+        await fs.ensureDir(path.dirname(tempBackupPath));
+        await fs.copy(modifiedFile.path, tempBackupPath, { overwrite: true });
+      }
+    }
+
+    return { tempBackupDir, tempModifiedBackupDir };
+  }
+
+  /**
+   * Install official (non-custom) modules.
+   * @param {Object} config - Installation configuration
+   * @param {Object} paths - InstallPaths instance
+   * @param {string[]} officialModuleIds - Official module IDs to install
+   * @param {Function} addResult - Callback to record installation results
+   * @param {boolean} isQuickUpdate - Whether this is a quick update
+   * @param {Object} ctx - Shared context: { message, installedModuleNames }
+   */
+  async _installOfficialModules(config, paths, officialModuleIds, addResult, isQuickUpdate, officialModules, ctx) {
+    const { message, installedModuleNames } = ctx;
+
+    for (const moduleName of officialModuleIds) {
+      if (installedModuleNames.has(moduleName)) continue;
+      installedModuleNames.add(moduleName);
+
+      message(`${isQuickUpdate ? 'Updating' : 'Installing'} ${moduleName}...`);
+
+      const moduleConfig = officialModules.moduleConfigs[moduleName] || {};
+      await officialModules.install(
+        moduleName,
+        paths.scmDir,
+        (filePath) => {
+          this.installedFiles.add(filePath);
+        },
+        {
+          skipModuleInstaller: true,
+          moduleConfig: moduleConfig,
+          installer: this,
+          silent: true,
+        },
+      );
+
+      addResult(`Module: ${moduleName}`, 'ok', isQuickUpdate ? 'updated' : 'installed');
+    }
+  }
+
+  /**
+   * Install custom modules using CustomModules.install().
+   * Source paths come from this.customModules.paths (populated by discoverPaths).
+   */
+  async _installCustomModules(config, paths, addResult, officialModules, ctx) {
+    const { message, installedModuleNames } = ctx;
+    const isQuickUpdate = config.isQuickUpdate();
+
+    for (const [moduleName, sourcePath] of this.customModules.paths) {
+      if (installedModuleNames.has(moduleName)) continue;
+      installedModuleNames.add(moduleName);
+
+      message(`${isQuickUpdate ? 'Updating' : 'Installing'} ${moduleName}...`);
+
+      const collectedModuleConfig = officialModules.moduleConfigs[moduleName] || {};
+      const result = await this.customModules.install(moduleName, paths.scmDir, (filePath) => this.installedFiles.add(filePath), {
+        moduleConfig: collectedModuleConfig,
+      });
+
+      // Generate runtime config.yaml with merged values
+      await this.generateModuleConfigs(paths.scmDir, {
+        [moduleName]: { ...config.coreConfig, ...result.moduleConfig, ...collectedModuleConfig },
+      });
+
+      addResult(`Module: ${moduleName}`, 'ok', isQuickUpdate ? 'updated' : 'installed');
+    }
+  }
+
+  /**
+   * Read files-manifest.csv
+   * @param {string} scmDir - SCM installation directory
+   * @returns {Array} Array of file entries from files-manifest.csv
+   */
+  async readFilesManifest(scmDir) {
+    const filesManifestPath = path.join(scmDir, '_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) {
+      await prompts.log.warn('Could not read files-manifest.csv: ' + error.message);
+      return [];
+    }
+  }
+
+  /**
+   * Detect custom and modified files
+   * @param {string} scmDir - SCM installation directory
+   * @param {Array} existingFilesManifest - Previous files from files-manifest.csv
+   * @returns {Object} Object with customFiles and modifiedFiles arrays
+   */
+  async detectCustomFiles(scmDir, existingFilesManifest) {
+    const customFiles = [];
+    const modifiedFiles = [];
+
+    // Memory is always in _scm/_memory
+    const scmMemoryPath = '_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(scmDir, fileEntry.path);
+        installedFilesMap.set(path.normalize(absolutePath), {
+          hash: fileEntry.hash,
+          relativePath: fileEntry.path,
+        });
+      }
+    }
+
+    // Recursively scan scmDir 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(scmDir, 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(scmDir, '_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(scmMemoryPath + '/') && 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(scmDir);
+    return { customFiles, modifiedFiles };
+  }
+
+  /**
+   * Generate clean config.yaml files for each installed module
+   * @param {string} scmDir - SCM installation directory
+   * @param {Object} moduleConfigs - Collected configuration values
+   */
+  async generateModuleConfigs(scmDir, 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(scmDir, { 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(scmDir, 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 SCM 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);
+      }
+    }
+  }
+
+  /**
+   * Merge all module-help.csv files into a single scm-help.csv
+   * Scans all installed modules for module-help.csv and merges them
+   * Enriches agent info from agent-manifest.csv
+   * Output is written to _scm/_config/scm-help.csv
+   * @param {string} scmDir - SCM installation directory
+   */
+  async mergeModuleHelpCatalogs(scmDir) {
+    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(scmDir, '_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: scm:module:agent:name
+          const agentCommand = module ? `scm:${module}:agent:${agentName}` : `scm:agent:${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(scmDir, { 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-skills)
+    const coreModulePath = getSourcePath('core-skills');
+    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(scmDir, 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.SCM_VERBOSE_INSTALL === 'true') {
+            await prompts.log.message(`  Merged module-help from: ${moduleName}`);
+          }
+        } catch (error) {
+          await prompts.log.warn(`  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(scmDir, '_config');
+    await fs.ensureDir(outputDir);
+    const outputPath = path.join(outputDir, 'scm-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.SCM_VERBOSE_INSTALL === 'true') {
+      await prompts.log.message(`  Generated scm-help.csv: ${allRows.length} workflows`);
+    }
+  }
+
+  /**
+   * Render a consolidated install summary using prompts.note()
+   * @param {Array} results - Array of {step, status: 'ok'|'error'|'warn', detail}
+   * @param {Object} context - {scmDir, modules, ides, customFiles, modifiedFiles}
+   */
+  async renderInstallSummary(results, context = {}) {
+    const color = await prompts.getColor();
+    const selectedIdes = new Set((context.ides || []).map((ide) => String(ide).toLowerCase()));
+
+    // Build step lines with status indicators
+    const lines = [];
+    for (const r of results) {
+      let stepLabel = null;
+
+      if (r.status !== 'ok') {
+        stepLabel = r.step;
+      } else if (r.step === 'Core') {
+        stepLabel = 'SCM';
+      } else if (r.step.startsWith('Module: ')) {
+        stepLabel = r.step;
+      } else if (selectedIdes.has(String(r.step).toLowerCase())) {
+        stepLabel = r.step;
+      }
+
+      if (!stepLabel) {
+        continue;
+      }
+
+      let icon;
+      if (r.status === 'ok') {
+        icon = color.green('\u2713');
+      } else if (r.status === 'warn') {
+        icon = color.yellow('!');
+      } else {
+        icon = color.red('\u2717');
+      }
+      const detail = r.detail ? color.dim(` (${r.detail})`) : '';
+      lines.push(`  ${icon}  ${stepLabel}${detail}`);
+    }
+
+    if ((context.ides || []).length === 0) {
+      lines.push(`  ${color.green('\u2713')}  No IDE selected ${color.dim('(installed in _scm only)')}`);
+    }
+
+    // Context and warnings
+    lines.push('');
+    if (context.scmDir) {
+      lines.push(`  Installed to: ${color.dim(context.scmDir)}`);
+    }
+    if (context.customFiles && context.customFiles.length > 0) {
+      lines.push(`  ${color.cyan(`Custom files preserved: ${context.customFiles.length}`)}`);
+    }
+    if (context.modifiedFiles && context.modifiedFiles.length > 0) {
+      lines.push(`  ${color.yellow(`Modified files backed up (.bak): ${context.modifiedFiles.length}`)}`);
+    }
+
+    // Next steps
+    lines.push(
+      '',
+      '  Next steps:',
+      `    Read our new Docs Site: ${color.dim('https://docs.scm-method.org/')}`,
+      `    Join our Discord: ${color.dim('https://discord.gg/gk8jAdXWmj')}`,
+      `    Star us on GitHub: ${color.dim('https://github.com/scm-code-org/SCM-METHOD/')}`,
+      `    Subscribe on YouTube: ${color.dim('https://www.youtube.com/@SCMCode')}`,
+    );
+    if (context.ides && context.ides.length > 0) {
+      lines.push(`    Invoke the ${color.cyan('scm-help')} skill in your IDE Agent to get started`);
+    }
+
+    await prompts.note(lines.join('\n'), 'SCM is ready to use!');
+  }
+
+  /**
+   * 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 projectDir = path.resolve(config.directory);
+    const { scmDir } = await this.findBmadDir(projectDir);
+
+    // Check if scm directory exists
+    if (!(await fs.pathExists(scmDir))) {
+      throw new Error(`SCM not installed at ${scmDir}. Use regular install for first-time setup.`);
+    }
+
+    // Detect existing installation
+    const existingInstall = await ExistingInstall.detect(scmDir);
+    const installedModules = existingInstall.moduleIds;
+    const configuredIdes = existingInstall.ides;
+    const projectRoot = path.dirname(scmDir);
+
+    // Get custom module sources: first from --custom-content (re-cache from source), then from cache
+    const customModuleSources = new Map();
+    if (config.customContent?.sources?.length > 0) {
+      for (const source of config.customContent.sources) {
+        if (source.id && source.path && (await fs.pathExists(source.path))) {
+          customModuleSources.set(source.id, {
+            id: source.id,
+            name: source.name || source.id,
+            sourcePath: source.path,
+            cached: false, // From CLI, will be re-cached
+          });
+        }
+      }
+    }
+    const cacheDir = path.join(scmDir, '_config', 'custom');
+    if (await fs.pathExists(cacheDir)) {
+      const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
+
+      for (const cachedModule of cachedModules) {
+        const moduleId = cachedModule.name;
+        const cachedPath = path.join(cacheDir, moduleId);
+
+        // Skip if path doesn't exist (broken symlink, deleted dir) - avoids lstat ENOENT
+        if (!(await fs.pathExists(cachedPath))) {
+          continue;
+        }
+        if (!cachedModule.isDirectory()) {
+          continue;
+        }
+
+        // Skip if we already have this module from manifest
+        if (customModuleSources.has(moduleId)) {
+          continue;
+        }
+
+        // Check if this is an external official module - skip cache for those
+        const isExternal = await this.externalModuleManager.hasModule(moduleId);
+        if (isExternal) {
+          continue;
+        }
+
+        // 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: cachedPath,
+            cached: true,
+          });
+        }
+      }
+    }
+
+    // Get available modules (what we have source for)
+    const availableModulesData = await new OfficialModules().listAvailable();
+    const availableModules = [...availableModulesData.modules, ...availableModulesData.customModules];
+
+    // Add external official modules to available modules
+    const externalModules = await this.externalModuleManager.listAvailable();
+    for (const externalModule of externalModules) {
+      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) {
+      const sourcePath = customModule.sourcePath;
+      if (sourcePath && (await fs.pathExists(sourcePath)) && !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
+    const customModuleResult = await this.handleMissingCustomSources(
+      customModuleSources,
+      scmDir,
+      projectRoot,
+      'update',
+      installedModules,
+      config.skipPrompts || false,
+    );
+
+    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));
+
+    // Only update modules that are BOTH installed AND available (we have source for)
+    const modulesToUpdate = installedModules.filter((id) => availableModuleIds.has(id));
+    const skippedModules = installedModules.filter((id) => !availableModuleIds.has(id));
+
+    // Add custom modules that were kept without sources to the skipped modules
+    for (const keptModule of keptModulesWithoutSources) {
+      if (!skippedModules.includes(keptModule)) {
+        skippedModules.push(keptModule);
+      }
+    }
+
+    if (skippedModules.length > 0) {
+      await prompts.log.warn(`Skipping ${skippedModules.length} module(s) - no source available: ${skippedModules.join(', ')}`);
+    }
+
+    // Load existing configs and collect new fields (if any)
+    await prompts.log.info('Checking for new configuration options...');
+    const quickModules = new OfficialModules();
+    await quickModules.loadExistingConfig(projectDir);
+
+    let promptedForNewFields = false;
+
+    const corePrompted = await quickModules.collectModuleConfigQuick('core', projectDir, true);
+    if (corePrompted) {
+      promptedForNewFields = true;
+    }
+
+    for (const moduleName of modulesToUpdate) {
+      const modulePrompted = await quickModules.collectModuleConfigQuick(moduleName, projectDir, true);
+      if (modulePrompted) {
+        promptedForNewFields = true;
+      }
+    }
+
+    if (!promptedForNewFields) {
+      await prompts.log.success('All configuration is up to date, no new options to configure');
+    }
+
+    quickModules.collectedConfig._meta = {
+      version: require(path.join(getProjectRoot(), 'package.json')).version,
+      installDate: new Date().toISOString(),
+      lastModified: new Date().toISOString(),
+    };
+
+    // Build config and delegate to install()
+    const installConfig = {
+      directory: projectDir,
+      modules: modulesToUpdate,
+      ides: configuredIdes,
+      coreConfig: quickModules.collectedConfig.core,
+      moduleConfigs: quickModules.collectedConfig,
+      actionType: 'install',
+      _quickUpdate: true,
+      _preserveModules: skippedModules,
+      _customModuleSources: customModuleSources,
+      _existingModules: installedModules,
+      customContent: config.customContent,
+    };
+
+    await this.install(installConfig);
+
+    return {
+      success: true,
+      moduleCount: modulesToUpdate.length,
+      hadNewFields: promptedForNewFields,
+      modules: modulesToUpdate,
+      skippedModules: skippedModules,
+      ides: configuredIdes,
+    };
+  }
+
+  /**
+   * Uninstall SCM with selective removal options
+   * @param {string} directory - Project directory
+   * @param {Object} options - Uninstall options
+   * @param {boolean} [options.removeModules=true] - Remove _scm/ directory
+   * @param {boolean} [options.removeIdeConfigs=true] - Remove IDE configurations
+   * @param {boolean} [options.removeOutputFolder=false] - Remove user artifacts output folder
+   * @returns {Object} Result with success status and removed components
+   */
+  async uninstall(directory, options = {}) {
+    const projectDir = path.resolve(directory);
+    const { scmDir } = await this.findBmadDir(projectDir);
+
+    if (!(await fs.pathExists(scmDir))) {
+      return { success: false, reason: 'not-installed' };
+    }
+
+    // 1. DETECT: Read state BEFORE deleting anything
+    const existingInstall = await ExistingInstall.detect(scmDir);
+    const outputFolder = await this._readOutputFolder(scmDir);
+
+    const removed = { modules: false, ideConfigs: false, outputFolder: false };
+
+    // 2. IDE CLEANUP (before _scm/ deletion so configs are accessible)
+    if (options.removeIdeConfigs !== false) {
+      await this.uninstallIdeConfigs(projectDir, existingInstall, { silent: options.silent });
+      removed.ideConfigs = true;
+    }
+
+    // 3. OUTPUT FOLDER (only if explicitly requested)
+    if (options.removeOutputFolder === true && outputFolder) {
+      removed.outputFolder = await this.uninstallOutputFolder(projectDir, outputFolder);
+    }
+
+    // 4. SCM DIRECTORY (last, after everything that needs it)
+    if (options.removeModules !== false) {
+      removed.modules = await this.uninstallModules(projectDir);
+    }
+
+    return { success: true, removed, version: existingInstall.installed ? existingInstall.version : null };
+  }
+
+  /**
+   * Uninstall IDE configurations only
+   * @param {string} projectDir - Project directory
+   * @param {Object} existingInstall - Detection result from detector.detect()
+   * @param {Object} [options] - Options (e.g. { silent: true })
+   * @returns {Promise<Object>} Results from IDE cleanup
+   */
+  async uninstallIdeConfigs(projectDir, existingInstall, options = {}) {
+    await this.ideManager.ensureInitialized();
+    const cleanupOptions = { isUninstall: true, silent: options.silent };
+    const ideList = existingInstall.ides;
+    if (ideList.length > 0) {
+      return this.ideManager.cleanupByList(projectDir, ideList, cleanupOptions);
+    }
+    return this.ideManager.cleanup(projectDir, cleanupOptions);
+  }
+
+  /**
+   * Remove user artifacts output folder
+   * @param {string} projectDir - Project directory
+   * @param {string} outputFolder - Output folder name (relative)
+   * @returns {Promise<boolean>} Whether the folder was removed
+   */
+  async uninstallOutputFolder(projectDir, outputFolder) {
+    if (!outputFolder) return false;
+    const resolvedProject = path.resolve(projectDir);
+    const outputPath = path.resolve(resolvedProject, outputFolder);
+    if (!outputPath.startsWith(resolvedProject + path.sep)) {
+      return false;
+    }
+    if (await fs.pathExists(outputPath)) {
+      await fs.remove(outputPath);
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Remove the _scm/ directory
+   * @param {string} projectDir - Project directory
+   * @returns {Promise<boolean>} Whether the directory was removed
+   */
+  async uninstallModules(projectDir) {
+    const { scmDir } = await this.findBmadDir(projectDir);
+    if (await fs.pathExists(scmDir)) {
+      await fs.remove(scmDir);
+      return true;
+    }
+    return false;
+  }
+
+  /**
+   * Get installation status
+   */
+  async getStatus(directory) {
+    const projectDir = path.resolve(directory);
+    const { scmDir } = await this.findBmadDir(projectDir);
+    return await ExistingInstall.detect(scmDir);
+  }
+
+  /**
+   * Get available modules
+   */
+  async getAvailableModules() {
+    return await new OfficialModules().listAvailable();
+  }
+
+  /**
+   * Get the configured output folder name for a project
+   * Resolves scmDir internally from projectDir
+   * @param {string} projectDir - Project directory
+   * @returns {string} Output folder name (relative, default: '_scm-output')
+   */
+  async getOutputFolder(projectDir) {
+    const { scmDir } = await this.findBmadDir(projectDir);
+    return this._readOutputFolder(scmDir);
+  }
+
+  /**
+   * Handle missing custom module sources interactively
+   * @param {Map} customModuleSources - Map of custom module ID to info
+   * @param {string} scmDir - SCM 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)
+   * @param {boolean} [skipPrompts=false] - Skip interactive prompts and keep all modules with missing sources
+   * @returns {Object} Object with validCustomModules array and keptModulesWithoutSources array
+   */
+  async handleMissingCustomSources(customModuleSources, scmDir, projectRoot, operation, installedModules, skipPrompts = false) {
+    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: [],
+      };
+    }
+
+    // Non-interactive mode: keep all modules with missing sources
+    if (skipPrompts) {
+      for (const missing of customModulesWithMissingSources) {
+        keptModulesWithoutSources.push(missing.id);
+      }
+      return { validCustomModules, keptModulesWithoutSources };
+    }
+
+    await prompts.log.warn(`Found ${customModulesWithMissingSources.length} custom module(s) with missing sources:`);
+
+    let keptCount = 0;
+    let updatedCount = 0;
+    let removedCount = 0;
+
+    for (const missing of customModulesWithMissingSources) {
+      await prompts.log.message(
+        `${missing.name} (${missing.id})\n  Original source: ${missing.relativePath}\n  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
+            },
+          });
+
+          // Defensive: handleCancel should have exited, but guard against symbol propagation
+          if (typeof newSourcePath !== 'string') {
+            keptCount++;
+            keptModulesWithoutSources.push(missing.id);
+            continue;
+          }
+
+          // 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(scmDir, missing.info);
+
+          validCustomModules.push({
+            id: missing.id,
+            name: missing.name,
+            path: resolvedPath,
+            info: missing.info,
+          });
+
+          updatedCount++;
+          await prompts.log.success('Updated source location');
+
+          break;
+        }
+        case 'remove': {
+          // Extra confirmation for destructive remove
+          await prompts.log.error(
+            `WARNING: This will PERMANENTLY DELETE "${missing.name}" and all its files!\n  Module location: ${path.join(scmDir, missing.id)}`,
+          );
+
+          const confirmDelete = await prompts.confirm({
+            message: 'Are you absolutely sure you want to delete this module?',
+            default: false,
+          });
+
+          if (confirmDelete) {
+            const typedConfirm = await prompts.text({
+              message: 'Type "DELETE" to confirm permanent deletion:',
+              validate: (input) => {
+                if (input !== 'DELETE') {
+                  return '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(scmDir, missing.id);
+              if (await fs.pathExists(modulePath)) {
+                const fsExtra = require('fs-extra');
+                await fsExtra.remove(modulePath);
+                await prompts.log.warn(`Deleted module directory: ${path.relative(projectRoot, modulePath)}`);
+              }
+
+              await this.manifest.removeModule(scmDir, missing.id);
+              await this.manifest.removeCustomModule(scmDir, missing.id);
+              await prompts.log.warn('Removed from manifest');
+
+              // Also remove from installedModules list
+              if (installedModules && installedModules.includes(missing.id)) {
+                const index = installedModules.indexOf(missing.id);
+                if (index !== -1) {
+                  installedModules.splice(index, 1);
+                }
+              }
+
+              removedCount++;
+              await prompts.log.error(`"${missing.name}" has been permanently removed`);
+            } else {
+              await prompts.log.message('Removal cancelled - module will be kept');
+              keptCount++;
+            }
+          } else {
+            await prompts.log.message('Removal cancelled - module will be kept');
+            keptCount++;
+          }
+
+          break;
+        }
+        case 'keep': {
+          keptCount++;
+          keptModulesWithoutSources.push(missing.id);
+          await prompts.log.message('Module will be kept as-is');
+
+          break;
+        }
+        // No default
+      }
+    }
+
+    // Show summary
+    if (keptCount > 0 || updatedCount > 0 || removedCount > 0) {
+      let summary = 'Summary for custom modules with missing sources:';
+      if (keptCount > 0) summary += `\n  • ${keptCount} module(s) kept as-is`;
+      if (updatedCount > 0) summary += `\n  • ${updatedCount} module(s) updated with new sources`;
+      if (removedCount > 0) summary += `\n  • ${removedCount} module(s) permanently deleted`;
+      await prompts.log.message(summary);
+    }
+
+    return {
+      validCustomModules,
+      keptModulesWithoutSources,
+    };
+  }
+
+  /**
+   * Find the scm installation directory in a project
+   * Always uses the standard _scm folder name
+   * @param {string} projectDir - Project directory
+   * @returns {Promise<Object>} { scmDir: string }
+   */
+  async findBmadDir(projectDir) {
+    const scmDir = path.join(projectDir, SCM_FOLDER_NAME);
+    return { scmDir };
+  }
+
+  /**
+   * Read the output_folder setting from module config files
+   * Checks bmm/config.yaml first, then other module configs
+   * @param {string} scmDir - SCM installation directory
+   * @returns {string} Output folder path or default
+   */
+  async _readOutputFolder(scmDir) {
+    const yaml = require('yaml');
+
+    // Check bmm/config.yaml first (most common)
+    const bmmConfigPath = path.join(scmDir, 'bmm', 'config.yaml');
+    if (await fs.pathExists(bmmConfigPath)) {
+      try {
+        const content = await fs.readFile(bmmConfigPath, 'utf8');
+        const config = yaml.parse(content);
+        if (config && config.output_folder) {
+          // Strip {project-root}/ prefix if present
+          return config.output_folder.replace(/^\{project-root\}[/\\]/, '');
+        }
+      } catch {
+        // Fall through to other modules
+      }
+    }
+
+    // Scan other module config.yaml files
+    try {
+      const entries = await fs.readdir(scmDir, { withFileTypes: true });
+      for (const entry of entries) {
+        if (!entry.isDirectory() || entry.name === 'bmm' || entry.name.startsWith('_')) continue;
+        const configPath = path.join(scmDir, entry.name, 'config.yaml');
+        if (await fs.pathExists(configPath)) {
+          try {
+            const content = await fs.readFile(configPath, 'utf8');
+            const config = yaml.parse(content);
+            if (config && config.output_folder) {
+              return config.output_folder.replace(/^\{project-root\}[/\\]/, '');
+            }
+          } catch {
+            // Continue scanning
+          }
+        }
+      }
+    } catch {
+      // Directory scan failed
+    }
+
+    // Default fallback
+    return '_scm-output';
+  }
+
+  /**
+   * 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;
+  }
+}
+
+module.exports = { Installer };