fix(installer): preserve stale installed modules on update

test/test-installation-components.js

@@ -164,6 +164,39 @@ async function runTests() {
 
   console.log('');
 
+  // ============================================================
+  // Test 4b: Preserve installed modules with no source
+  // ============================================================
+  console.log(`${colors.yellow}Test Suite 4b: Preserve Installed Modules Without Source${colors.reset}\n`);
+
+  let staleInstallRoot;
+  try {
+    staleInstallRoot = await fs.mkdtemp(path.join(os.tmpdir(), 'bmad-stale-module-'));
+    const staleBmadDir = path.join(staleInstallRoot, '_bmad');
+    const staleModuleDir = path.join(staleBmadDir, 'baut');
+    await fs.ensureDir(staleModuleDir);
+    await fs.writeFile(path.join(staleModuleDir, 'marker.txt'), 'keep me\n', 'utf8');
+
+    const ui = new (require('../tools/installer/ui').UI)();
+    const unavailable = await ui._findUnavailableInstalledModules(new Set(['core', 'bmm', 'baut']), staleBmadDir);
+    assert(unavailable.length === 1 && unavailable[0] === 'baut', 'UI detects stale installed modules with no current source');
+
+    const installer = new Installer();
+    await installer._removeDeselectedModules(
+      { moduleIds: ['core', 'bmm', 'baut'] },
+      { modules: ['core', 'bmm'] },
+      { moduleDir: (moduleId) => path.join(staleBmadDir, moduleId) },
+      ['baut'],
+    );
+    assert(await fs.pathExists(path.join(staleModuleDir, 'marker.txt')), 'Preserved modules are not removed during modify/update installs');
+  } catch (error) {
+    assert(false, 'Installed modules with no source are preserved during update', error.message);
+  } finally {
+    if (staleInstallRoot) await fs.remove(staleInstallRoot).catch(() => {});
+  }
+
+  console.log('');
+
   // ============================================================
   // Test 5: Kiro Native Skills Install
   // ============================================================

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);
       }
@@ -144,10 +144,11 @@ 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);

tools/installer/ui.js

@@ -110,6 +110,44 @@ async function getModuleVersion(moduleCode, { repoUrl = null, registryDefault =
  * UI utilities for the installer
  */
 class UI {
+  async _findUnavailableInstalledModules(installedModuleIds = new Set(), bmadDir) {
+    const { OfficialModules } = require('./modules/official-modules');
+    const availableModulesData = await new OfficialModules().listAvailable();
+    const availableModules = [...availableModulesData.modules];
+
+    const externalManager = new ExternalModuleManager();
+    const externalModules = await externalManager.listAvailable();
+    for (const externalModule of externalModules) {
+      if (installedModuleIds.has(externalModule.code) && !availableModules.some((m) => m.id === externalModule.code)) {
+        availableModules.push({
+          id: externalModule.code,
+          name: externalModule.name,
+          isExternal: true,
+          fromExternal: true,
+        });
+      }
+    }
+
+    const { CustomModuleManager } = require('./modules/custom-module-manager');
+    const customMgr = new CustomModuleManager();
+    for (const moduleId of installedModuleIds) {
+      if (!availableModules.some((m) => m.id === moduleId)) {
+        const customSource = await customMgr.findModuleSourceByCode(moduleId, { bmadDir });
+        if (customSource) {
+          availableModules.push({
+            id: moduleId,
+            name: moduleId,
+            isExternal: true,
+            fromCustom: true,
+          });
+        }
+      }
+    }
+
+    const availableModuleIds = new Set(availableModules.map((m) => m.id));
+    return [...installedModuleIds].filter((id) => !availableModuleIds.has(id));
+  }
+
   /**
    * Prompt for installation configuration
    * @param {Object} options - Command-line options from install command
@@ -273,6 +311,15 @@ class UI {
           selectedModules.unshift('core');
         }
 
+        const preservedModules = await this._findUnavailableInstalledModules(installedModuleIds, bmadDir);
+        if (preservedModules.length > 0) {
+          const preservedSet = new Set(preservedModules);
+          selectedModules = selectedModules.filter((moduleName) => !preservedSet.has(moduleName));
+          await prompts.log.warn(
+            `Retaining ${preservedModules.length} installed module(s) with no source available: ${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 +364,7 @@ class UI {
           setOverrides,
           skipPrompts: options.yes || false,
           channelOptions,
+          _preserveModules: preservedModules,
         };
       }
     }