fix(installer): preserve stale installed modules during update

tools/installer/core/installer.js

@@ -54,7 +54,7 @@ class Installer {
       }
 
       if (existingInstall.installed) {
-        await this._removeDeselectedModules(existingInstall, config, paths);
+        await this._removeDeselectedModules(existingInstall, config, paths, originalConfig._preserveModules || []);
         updateState = await this._prepareUpdateState(paths, config, existingInstall, officialModules);
         await this._removeDeselectedIdes(existingInstall, config, paths);
       }
@@ -76,25 +76,23 @@ class Installer {
       const results = [];
       const addResult = (step, status, detail = '', meta = {}) => results.push({ step, status, detail, ...meta });
 
-      // Capture previously installed skill IDs before they get overwritten
-      const previousSkillIds = new Set();
-      const prevCsvPath = path.join(paths.bmadDir, '_config', 'skill-manifest.csv');
-      if (await fs.pathExists(prevCsvPath)) {
-        try {
-          const csvParse = require('csv-parse/sync');
-          const content = await fs.readFile(prevCsvPath, 'utf8');
-          const records = csvParse.parse(content, { columns: true, skip_empty_lines: true });
-          for (const r of records) {
-            if (r.canonicalId) previousSkillIds.add(r.canonicalId);
-          }
-        } catch (error) {
-          await prompts.log.warn(`Failed to parse skill-manifest.csv: ${error.message}`);
-        }
-      }
+      // Capture previously installed skill rows before they get overwritten
+      const preservedModules = originalConfig._preserveModules || [];
+      const previousSkillManifestRows = await this._readSkillManifestRows(paths.bmadDir);
+      const previousSkillIds = this._getPreviousSkillIdsForCleanup(previousSkillManifestRows, preservedModules);
 
       const allModules = config.modules || [];
 
-      await this._installAndConfigure(config, originalConfig, paths, allModules, allModules, addResult, officialModules);
+      await this._installAndConfigure(
+        config,
+        originalConfig,
+        paths,
+        allModules,
+        allModules,
+        addResult,
+        officialModules,
+        previousSkillManifestRows,
+      );
 
       await this._setupIdes(config, allModules, paths, addResult, previousSkillIds);
 
@@ -144,10 +142,11 @@ class Installer {
    * 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) {
+  async _removeDeselectedModules(existingInstall, config, paths, preservedModules = []) {
     const previouslyInstalled = new Set(existingInstall.moduleIds);
     const newlySelected = new Set(config.modules || []);
-    const toRemove = [...previouslyInstalled].filter((m) => !newlySelected.has(m) && m !== 'core');
+    const preserved = new Set(preservedModules);
+    const toRemove = [...previouslyInstalled].filter((m) => !newlySelected.has(m) && m !== 'core' && !preserved.has(m));
 
     for (const moduleId of toRemove) {
       const modulePath = paths.moduleDir(moduleId);
@@ -212,7 +211,16 @@ class Installer {
   /**
    * Install modules, create directories, generate configs and manifests.
    */
-  async _installAndConfigure(config, originalConfig, paths, officialModuleIds, allModules, addResult, officialModules) {
+  async _installAndConfigure(
+    config,
+    originalConfig,
+    paths,
+    officialModuleIds,
+    allModules,
+    addResult,
+    officialModules,
+    previousSkillManifestRows = [],
+  ) {
     const isQuickUpdate = config.isQuickUpdate();
     const moduleConfigs = officialModules.moduleConfigs;
 
@@ -291,25 +299,29 @@ class Installer {
 
         message('Generating manifests...');
         const manifestGen = new ManifestGenerator();
+        const preservedModules = originalConfig._preserveModules || [];
 
         const allModulesForManifest = config.isQuickUpdate()
           ? originalConfig._existingModules || allModules || []
-          : originalConfig._preserveModules
-            ? [...allModules, ...originalConfig._preserveModules]
+          : preservedModules.length > 0
+            ? [...allModules, ...preservedModules]
             : allModules || [];
 
         let modulesForCsvPreserve;
         if (config.isQuickUpdate()) {
           modulesForCsvPreserve = originalConfig._existingModules || allModules || [];
         } else {
-          modulesForCsvPreserve = originalConfig._preserveModules ? [...allModules, ...originalConfig._preserveModules] : allModules;
+          modulesForCsvPreserve = preservedModules.length > 0 ? [...allModules, ...preservedModules] : allModules;
         }
 
+        await this._trackPreservedModuleFiles(paths.bmadDir, preservedModules);
+
         await manifestGen.generateManifests(paths.bmadDir, allModulesForManifest, [...this.installedFiles], {
           ides: config.ides || [],
           preservedModules: modulesForCsvPreserve,
           moduleConfigs,
         });
+        await this._appendPreservedSkillManifestRows(paths.bmadDir, previousSkillManifestRows, preservedModules);
 
         // Apply post-install --set TOML patches. Runs after writeCentralConfig
         // (inside generateManifests above) so the patch operates on the
@@ -411,6 +423,62 @@ class Installer {
     }
   }
 
+  async _readSkillManifestRows(bmadDir) {
+    const csvPath = path.join(bmadDir, '_config', 'skill-manifest.csv');
+    if (!(await fs.pathExists(csvPath))) return [];
+
+    try {
+      const csvParse = require('csv-parse/sync');
+      const content = await fs.readFile(csvPath, 'utf8');
+      return csvParse.parse(content, { columns: true, skip_empty_lines: true });
+    } catch (error) {
+      await prompts.log.warn(`Failed to parse skill-manifest.csv: ${error.message}`);
+      return [];
+    }
+  }
+
+  _getPreviousSkillIdsForCleanup(previousRows, preservedModules = []) {
+    const preservedModuleSet = new Set(preservedModules || []);
+    const ids = new Set();
+    for (const row of previousRows || []) {
+      if (row.canonicalId && !preservedModuleSet.has(row.module)) {
+        ids.add(row.canonicalId);
+      }
+    }
+    return ids;
+  }
+
+  async _appendPreservedSkillManifestRows(bmadDir, previousRows, preservedModules = []) {
+    if (!previousRows || previousRows.length === 0 || preservedModules.length === 0) return;
+
+    const preservedModuleSet = new Set(preservedModules);
+    const rowsToPreserve = previousRows.filter((row) => row.canonicalId && row.module && preservedModuleSet.has(row.module));
+    if (rowsToPreserve.length === 0) return;
+
+    const csvPath = path.join(bmadDir, '_config', 'skill-manifest.csv');
+    if (!(await fs.pathExists(csvPath))) return;
+
+    const currentRows = await this._readSkillManifestRows(bmadDir);
+    const activeIds = new Set(currentRows.map((row) => row.canonicalId).filter(Boolean));
+    const appendedRows = [];
+
+    for (const row of rowsToPreserve) {
+      if (activeIds.has(row.canonicalId)) continue;
+      activeIds.add(row.canonicalId);
+      appendedRows.push(
+        [row.canonicalId, row.name || row.canonicalId, row.description || '', row.module, row.path || '']
+          .map((field) => this.escapeCSVField(field))
+          .join(','),
+      );
+    }
+
+    if (appendedRows.length === 0) return;
+
+    const currentContent = await fs.readFile(csvPath, 'utf8');
+    const prefix = currentContent.endsWith('\n') ? currentContent : `${currentContent}\n`;
+    await fs.writeFile(csvPath, prefix + appendedRows.join('\n') + '\n', 'utf8');
+  }
+
   /**
    * Restore custom and modified files that were backed up before the update.
    * No-op for fresh installs (updateState is null).
@@ -597,6 +665,15 @@ class Installer {
     }
   }
 
+  async _trackPreservedModuleFiles(bmadDir, preservedModules = []) {
+    for (const moduleName of preservedModules) {
+      const modulePath = path.join(bmadDir, moduleName);
+      if (await fs.pathExists(modulePath)) {
+        await this._trackFilesRecursive(modulePath);
+      }
+    }
+  }
+
   /**
    * Install official (non-custom) modules.
    * @param {Object} config - Installation configuration

tools/installer/ide/_config-driven.js

@@ -501,7 +501,7 @@ class ConfigDrivenIdeSetup {
 
     // Build removal set: previously installed skills + removals.txt entries
     let removalSet;
-    if (options.previousSkillIds && options.previousSkillIds.size > 0) {
+    if (options.previousSkillIds) {
       // Install/update flow: use pre-captured skill IDs (before manifest was overwritten)
       removalSet = new Set(options.previousSkillIds);
       if (resolvedBmadDir) {
@@ -547,7 +547,7 @@ class ConfigDrivenIdeSetup {
       // previousSkillIds — full uninstall or per-IDE removal via
       // cleanupByList), don't spare anything; the IDE itself is going away,
       // so its pointers should go with it.
-      const isInstallFlow = options.previousSkillIds && options.previousSkillIds.size > 0;
+      const isInstallFlow = !!options.previousSkillIds;
       const activeSkillIds = isInstallFlow ? await this._readActiveSkillIds(resolvedBmadDir) : new Set();
       const extension = this.installerConfig.commands_extension || '.md';
       await this.cleanupCommandPointers(

tools/installer/ui.js

@@ -110,6 +110,44 @@ async function getModuleVersion(moduleCode, { repoUrl = null, registryDefault =
  * UI utilities for the installer
  */
 class UI {
+  async _retainUnavailableInstalledModules(selectedModules, installedModuleIds, bmadDir, options = {}) {
+    const { OfficialModules } = require('./modules/official-modules');
+    const officialCodes = new Set(['core']);
+
+    const builtInModules = (await new OfficialModules().listAvailable()).modules || [];
+    for (const mod of builtInModules) {
+      officialCodes.add(mod.id);
+    }
+
+    const externalManager = new ExternalModuleManager();
+    const registryModules = await externalManager.listAvailable();
+    for (const mod of registryModules) {
+      officialCodes.add(mod.code);
+    }
+
+    const { CustomModuleManager } = require('./modules/custom-module-manager');
+    const customMgr = new CustomModuleManager();
+    const selectedSet = new Set(selectedModules);
+    const preserveModules = [];
+
+    for (const moduleId of installedModuleIds) {
+      if (moduleId === 'core') continue;
+      if (!selectedSet.has(moduleId) && !options.preserveUnselected) continue;
+      if (officialCodes.has(moduleId)) continue;
+
+      const customSource = await customMgr.findModuleSourceByCode(moduleId, { bmadDir });
+      if (!customSource) {
+        preserveModules.push(moduleId);
+      }
+    }
+
+    const preservedSet = new Set(preserveModules);
+    return {
+      selectedModules: selectedModules.filter((moduleId) => !preservedSet.has(moduleId)),
+      preserveModules,
+    };
+  }
+
   /**
    * Prompt for installation configuration
    * @param {Object} options - Command-line options from install command
@@ -273,6 +311,18 @@ class UI {
           selectedModules.unshift('core');
         }
 
+        const retainedModuleResult = await this._retainUnavailableInstalledModules(selectedModules, installedModuleIds, bmadDir, {
+          preserveUnselected: options.yes && !options.modules,
+        });
+        selectedModules = retainedModuleResult.selectedModules;
+        const preservedModules = retainedModuleResult.preserveModules;
+
+        if (preservedModules.length > 0) {
+          await prompts.log.warn(
+            `Retaining ${preservedModules.length} installed module(s) with no available source: ${preservedModules.join(', ')}`,
+          );
+        }
+
         // For existing installs, resolve per-module update decisions BEFORE
         // we clone anything. Reads the existing manifest's recorded channel
         // per module and prompts the user on available upgrades (patch/minor
@@ -317,6 +367,7 @@ class UI {
           setOverrides,
           skipPrompts: options.yes || false,
           channelOptions,
+          _preserveModules: preservedModules,
         };
       }
     }