Fix: --custom-content flag and workflow config.yaml copying (#1651)

* fix custom install bug

* fix manager.js

* From PR #1624: added empty module.yaml handling (skip + warn) and removed paths from the config to match promptCustomContentSource()

* fix: custom-content quick-update ENOENT, pass --custom-content through, add PR#1624 improvements to allow update installs to work using non-interactive mode

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

@@ -527,8 +527,13 @@ class Installer {
             const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
 
             for (const cachedModule of cachedModules) {
-              if (cachedModule.isDirectory()) {
               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 (customModulePaths.has(moduleId)) {
@@ -542,15 +547,12 @@ class Installer {
                 continue;
               }
 
-                const cachedPath = path.join(cacheDir, moduleId);
-
               // Check if this is actually a custom module (has module.yaml)
               const moduleYamlPath = path.join(cachedPath, 'module.yaml');
               if (await fs.pathExists(moduleYamlPath)) {
                 customModulePaths.set(moduleId, cachedPath);
               }
             }
-            }
 
             // Update module manager with the new custom module paths from cache
             this.moduleManager.setCustomModulePaths(customModulePaths);
@@ -609,8 +611,13 @@ class Installer {
           const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
 
           for (const cachedModule of cachedModules) {
-            if (cachedModule.isDirectory()) {
             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 (customModulePaths.has(moduleId)) {
@@ -624,15 +631,12 @@ class Installer {
               continue;
             }
 
-              const cachedPath = path.join(cacheDir, moduleId);
-
             // Check if this is actually a custom module (has module.yaml)
             const moduleYamlPath = path.join(cachedPath, 'module.yaml');
             if (await fs.pathExists(moduleYamlPath)) {
               customModulePaths.set(moduleId, cachedPath);
             }
           }
-          }
 
           // Update module manager with the new custom module paths from cache
           this.moduleManager.setCustomModulePaths(customModulePaths);
@@ -949,12 +953,11 @@ class Installer {
               if (!isCustomModule && config._customModuleSources && config._customModuleSources.has(moduleName)) {
                 customInfo = config._customModuleSources.get(moduleName);
                 isCustomModule = true;
-                if (
+                if (customInfo.sourcePath && !customInfo.path) {
-                  customInfo.sourcePath &&
+                  customInfo.path = path.isAbsolute(customInfo.sourcePath)
-                  (customInfo.sourcePath.startsWith('_config') || customInfo.sourcePath.includes('_config/custom')) &&
+                    ? customInfo.sourcePath
-                  !customInfo.path
+                    : path.join(bmadDir, customInfo.sourcePath);
-                )
+                }
-                  customInfo.path = customInfo.sourcePath;
               }
 
               // Finally check regular custom content
@@ -2373,15 +2376,35 @@ class Installer {
       const configuredIdes = existingInstall.ides || [];
       const projectRoot = path.dirname(bmadDir);
 
-      // Get custom module sources from cache
+      // 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(bmadDir, '_config', 'custom');
       if (await fs.pathExists(cacheDir)) {
         const cachedModules = await fs.readdir(cacheDir, { withFileTypes: true });
 
         for (const cachedModule of cachedModules) {
-          if (cachedModule.isDirectory()) {
           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)) {
@@ -2395,8 +2418,6 @@ class Installer {
             continue;
           }
 
-            const cachedPath = path.join(cacheDir, moduleId);
-
           // Check if this is actually a custom module (has module.yaml)
           const moduleYamlPath = path.join(cachedPath, 'module.yaml');
           if (await fs.pathExists(moduleYamlPath)) {
@@ -2410,7 +2431,6 @@ class Installer {
           }
         }
       }
-      }
 
       // Load saved IDE configurations
       const savedIdeConfigs = await this.ideConfigManager.loadAllIdeConfigs(bmadDir);
@@ -2544,6 +2564,7 @@ class Installer {
         _savedIdeConfigs: savedIdeConfigs, // Pass saved IDE configs to installer
         _customModuleSources: customModuleSources, // Pass custom module sources for updates
         _existingModules: installedModules, // Pass all installed modules for manifest generation
+        customContent: config.customContent, // Pass through for re-caching from source
       };
 
       // Call the standard install method

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

@@ -734,8 +734,10 @@ class ModuleManager {
         continue;
       }
 
-      // Skip config.yaml templates - we'll generate clean ones with actual values
+      // Skip module root config.yaml only - generated by config collector with actual values
-      if (file === 'config.yaml' || file.endsWith('/config.yaml')) {
+      // Workflow-level config.yaml (e.g. workflows/orchestrate-story/config.yaml) must be copied
+      // for custom modules that use workflow-specific configuration
+      if (file === 'config.yaml') {
         continue;
       }
 

tools/cli/lib/ui.js

@@ -245,11 +245,48 @@ class UI {
 
       // Handle quick update separately
       if (actionType === 'quick-update') {
-        // Quick update doesn't install custom content - just updates existing modules
+        // Pass --custom-content through so installer can re-cache if cache is missing
+        let customContentForQuickUpdate = { hasCustomContent: false };
+        if (options.customContent) {
+          const paths = options.customContent
+            .split(',')
+            .map((p) => p.trim())
+            .filter(Boolean);
+          if (paths.length > 0) {
+            const customPaths = [];
+            const selectedModuleIds = [];
+            const sources = [];
+            for (const customPath of paths) {
+              const expandedPath = this.expandUserPath(customPath);
+              const validation = this.validateCustomContentPathSync(expandedPath);
+              if (validation) continue;
+              let moduleMeta;
+              try {
+                const moduleYamlPath = path.join(expandedPath, 'module.yaml');
+                moduleMeta = require('yaml').parse(await fs.readFile(moduleYamlPath, 'utf-8'));
+              } catch {
+                continue;
+              }
+              if (!moduleMeta?.code) continue;
+              customPaths.push(expandedPath);
+              selectedModuleIds.push(moduleMeta.code);
+              sources.push({ path: expandedPath, id: moduleMeta.code, name: moduleMeta.name || moduleMeta.code });
+            }
+            if (customPaths.length > 0) {
+              customContentForQuickUpdate = {
+                hasCustomContent: true,
+                selected: true,
+                sources,
+                selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
+                selectedModuleIds,
+              };
+            }
+          }
+        }
         return {
           actionType: 'quick-update',
           directory: confirmedDirectory,
-          customContent: { hasCustomContent: false },
+          customContent: customContentForQuickUpdate,
           skipPrompts: options.yes || false,
         };
       }
@@ -305,6 +342,7 @@ class UI {
           // Build custom content config similar to promptCustomContentSource
           const customPaths = [];
           const selectedModuleIds = [];
+          const sources = [];
 
           for (const customPath of paths) {
             const expandedPath = this.expandUserPath(customPath);
@@ -326,6 +364,11 @@ class UI {
               continue;
             }
 
+            if (!moduleMeta) {
+              await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml is empty`);
+              continue;
+            }
+
             if (!moduleMeta.code) {
               await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml missing 'code' field`);
               continue;
@@ -333,6 +376,11 @@ class UI {
 
             customPaths.push(expandedPath);
             selectedModuleIds.push(moduleMeta.code);
+            sources.push({
+              path: expandedPath,
+              id: moduleMeta.code,
+              name: moduleMeta.name || moduleMeta.code,
+            });
           }
 
           if (customPaths.length > 0) {
@@ -340,7 +388,9 @@ class UI {
               selectedCustomModules: selectedModuleIds,
               customContentConfig: {
                 hasCustomContent: true,
-                paths: customPaths,
+                selected: true,
+                sources,
+                selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
                 selectedModuleIds: selectedModuleIds,
               },
             };
@@ -446,6 +496,7 @@ class UI {
       // Build custom content config similar to promptCustomContentSource
       const customPaths = [];
       const selectedModuleIds = [];
+      const sources = [];
 
       for (const customPath of paths) {
         const expandedPath = this.expandUserPath(customPath);
@@ -467,6 +518,11 @@ class UI {
           continue;
         }
 
+        if (!moduleMeta) {
+          await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml is empty`);
+          continue;
+        }
+
         if (!moduleMeta.code) {
           await prompts.log.warn(`Skipping custom content path: ${customPath} - module.yaml missing 'code' field`);
           continue;
@@ -474,12 +530,19 @@ class UI {
 
         customPaths.push(expandedPath);
         selectedModuleIds.push(moduleMeta.code);
+        sources.push({
+          path: expandedPath,
+          id: moduleMeta.code,
+          name: moduleMeta.name || moduleMeta.code,
+        });
       }
 
       if (customPaths.length > 0) {
         customContentConfig = {
           hasCustomContent: true,
-          paths: customPaths,
+          selected: true,
+          sources,
+          selectedFiles: customPaths.map((p) => path.join(p, 'module.yaml')),
           selectedModuleIds: selectedModuleIds,
         };
       }