Fix #990: Enable custom module discovery in installer

- Fix 'installedModules is not defined' error in compileAgents()
- Add manifest regeneration during compilation to discover custom content
- Change manifest generator to scan all directories dynamically
- Fix ManifestGenerator import to use destructuring
- Handle custom modules without installer source gracefully

This enables custom workflows/agents/tasks in .bmad/custom/ to be
automatically discovered and generate proper .claude/commands/ files.

Changes:
- installer.js: Add manifest regeneration, fix imports, handle custom modules
- manifest-generator.js: Scan all directories instead of hardcoded list

Fixes #990

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

@@ -1787,7 +1787,17 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
             // Rebuild module agents from installer source
             const agentsPath = path.join(modulePath, 'agents');
             if (await fs.pathExists(agentsPath)) {
-              await this.rebuildAgentFiles(modulePath, entry.name);
+              // Check if this module has source in the installer
+              const sourceAgentsPath =
+                entry.name === 'core'
+                  ? path.join(getModulePath('core'), 'agents')
+                  : path.join(getSourcePath(`modules/${entry.name}`), 'agents');
+
+              // Only rebuild if source exists in installer, otherwise skip (for custom modules)
+              if (await fs.pathExists(sourceAgentsPath)) {
+                await this.rebuildAgentFiles(modulePath, entry.name);
+              }
+
               const agentFiles = await fs.readdir(agentsPath);
               agentCount += agentFiles.filter((f) => f.endsWith('.md')).length;
             }
@@ -1812,9 +1822,16 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         spinner.succeed('No custom agents found to rebuild');
       }
 
-      // Skip full manifest regeneration during compileAgents to preserve custom agents
+      // Detect installed modules for manifest regeneration and IDE configuration
-      // Custom agents are already added to manifests during individual installation
+      spinner.start('Regenerating manifests...');
-      // Only regenerate YAML manifest for IDE updates if needed
+      const existingInstall = await this.detector.detect(bmadDir);
+      const installedModules = existingInstall.modules.map((m) => m.id);
+
+      // Regenerate manifests to include all discovered content (including custom)
+      const { ManifestGenerator } = require('./manifest-generator');
+      const manifestGen = new ManifestGenerator();
+
+      // Get existing IDE list from current manifest
       const existingManifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
       let existingIdes = [];
       if (await fs.pathExists(existingManifestPath)) {
@@ -1824,6 +1841,12 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         existingIdes = manifest.ides || [];
       }
 
+      await manifestGen.generateManifests(bmadDir, installedModules, [], {
+        ides: existingIdes,
+        preservedModules: [],
+      });
+      spinner.succeed('Manifests regenerated');
+
       // Update IDE configurations using the existing IDE list from manifest
       if (existingIdes && existingIdes.length > 0) {
         spinner.start('Updating IDE configurations...');

tools/cli/installers/lib/core/manifest-generator.js

@@ -87,20 +87,24 @@ class ManifestGenerator {
   }
 
   /**
-   * Collect all workflows from core and selected modules
+   * Collect all workflows from ALL directories in bmad installation
    * Scans the INSTALLED bmad directory, not the source
    */
   async collectWorkflows(selectedModules) {
     this.workflows = [];
 
-    // Use updatedModules which already includes deduplicated 'core' + selectedModules
+    // Scan all directories under bmad installation
-    for (const moduleName of this.updatedModules) {
+    const entries = await fs.readdir(this.bmadDir, { withFileTypes: true });
-      const modulePath = path.join(this.bmadDir, moduleName);
 
-      if (await fs.pathExists(modulePath)) {
+    for (const entry of entries) {
-        const moduleWorkflows = await this.getWorkflowsFromPath(modulePath, moduleName);
+      // Skip special directories that don't contain modules
-        this.workflows.push(...moduleWorkflows);
+      if (!entry.isDirectory() || entry.name === '_cfg' || entry.name === 'docs') {
+        continue;
       }
+
+      const modulePath = path.join(this.bmadDir, entry.name);
+      const moduleWorkflows = await this.getWorkflowsFromPath(modulePath, entry.name);
+      this.workflows.push(...moduleWorkflows);
     }
   }
 
@@ -175,23 +179,32 @@ class ManifestGenerator {
   }
 
   /**
-   * Collect all agents from core and selected modules
+   * Collect all agents from ALL directories in bmad installation
    * Scans the INSTALLED bmad directory, not the source
    */
   async collectAgents(selectedModules) {
     this.agents = [];
 
-    // Use updatedModules which already includes deduplicated 'core' + selectedModules
+    // Scan all directories under bmad installation
-    for (const moduleName of this.updatedModules) {
+    const entries = await fs.readdir(this.bmadDir, { withFileTypes: true });
-      const agentsPath = path.join(this.bmadDir, moduleName, 'agents');
 
+    for (const entry of entries) {
+      // Skip special directories that don't contain modules
+      if (!entry.isDirectory() || entry.name === '_cfg' || entry.name === 'docs') {
+        continue;
+      }
+
+      const modulePath = path.join(this.bmadDir, entry.name);
+
+      // Check for agents/ subdirectory in this module
+      const agentsPath = path.join(modulePath, 'agents');
       if (await fs.pathExists(agentsPath)) {
-        const moduleAgents = await this.getAgentsFromDir(agentsPath, moduleName);
+        const moduleAgents = await this.getAgentsFromDir(agentsPath, entry.name);
         this.agents.push(...moduleAgents);
       }
     }
 
-    // Get standalone agents from bmad/agents/ directory
+    // Also check for standalone agents in bmad/agents/ directory (top-level)
     const standaloneAgentsDir = path.join(this.bmadDir, 'agents');
     if (await fs.pathExists(standaloneAgentsDir)) {
       const agentDirs = await fs.readdir(standaloneAgentsDir, { withFileTypes: true });
@@ -283,18 +296,27 @@ class ManifestGenerator {
   }
 
   /**
-   * Collect all tasks from core and selected modules
+   * Collect all tasks from ALL directories in bmad installation
    * Scans the INSTALLED bmad directory, not the source
    */
   async collectTasks(selectedModules) {
     this.tasks = [];
 
-    // Use updatedModules which already includes deduplicated 'core' + selectedModules
+    // Scan all directories under bmad installation
-    for (const moduleName of this.updatedModules) {
+    const entries = await fs.readdir(this.bmadDir, { withFileTypes: true });
-      const tasksPath = path.join(this.bmadDir, moduleName, 'tasks');
 
+    for (const entry of entries) {
+      // Skip special directories that don't contain modules
+      if (!entry.isDirectory() || entry.name === '_cfg' || entry.name === 'docs') {
+        continue;
+      }
+
+      const modulePath = path.join(this.bmadDir, entry.name);
+
+      // Check for tasks/ subdirectory in this module
+      const tasksPath = path.join(modulePath, 'tasks');
       if (await fs.pathExists(tasksPath)) {
-        const moduleTasks = await this.getTasksFromDir(tasksPath, moduleName);
+        const moduleTasks = await this.getTasksFromDir(tasksPath, entry.name);
         this.tasks.push(...moduleTasks);
       }
     }