custom modules install after any non custom modules selected and after the core, manifest tracks custom modules separately to ensure always installed from the custom cache

tools/cli/installers/lib/modules/manager.js

@@ -29,6 +29,7 @@ class ModuleManager {
     this.xmlHandler = new XmlHandler();
     this.bmadFolderName = 'bmad'; // Default, can be overridden
     this.scanProjectForModules = options.scanProjectForModules !== false; // Default to true for backward compatibility
+    this.customModulePaths = new Map(); // Initialize custom module paths
   }
 
   /**
@@ -47,6 +48,14 @@ class ModuleManager {
     this.coreConfig = coreConfig;
   }
 
+  /**
+   * Set custom module paths for priority lookup
+   * @param {Map<string, string>} customModulePaths - Map of module ID to source path
+   */
+  setCustomModulePaths(customModulePaths) {
+    this.customModulePaths = customModulePaths;
+  }
+
   /**
    * Copy a file and replace _bmad placeholder with actual folder name
    * @param {string} sourcePath - Source file path
@@ -340,6 +349,11 @@ class ModuleManager {
   async findModuleSource(moduleName) {
     const projectRoot = getProjectRoot();
 
+    // First check custom module paths if they exist
+    if (this.customModulePaths && this.customModulePaths.has(moduleName)) {
+      return this.customModulePaths.get(moduleName);
+    }
+
     // First, check src/modules
     const srcModulePath = path.join(this.modulesSourcePath, moduleName);
     if (await fs.pathExists(srcModulePath)) {