fix(installer): port three main-branch patches and fix custom module routing

Port bug fixes that landed on main after this branch forked:

1. Remove dead .agent.yaml/.xml fallback logic from skill-manifest.js
   and simplify scanInstalledModules to hasAgents || hasSkills

2. Fix config paths (issue 55): add resolveConfigValue,
   cleanPromptValue, normalizeExistingValueForPrompt to prevent
   template duplication on re-prompt

3. Fix empty agent-manifest.csv: replace collectAgents/getAgentsFromDir
   with getAgentsFromDirRecursive that walks full module trees, fix 9
   BMM manifests type: skill → type: agent, add dead-code TODO to
   bmad-artifacts.js

4. Fix custom module install crash: discoverPaths was receiving the
   clean Config (which strips customContent) instead of customConfig

src/bmm-skills/1-analysis/bmad-agent-analyst/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-analyst
 displayName: Mary
 title: Business Analyst

src/bmm-skills/1-analysis/bmad-agent-tech-writer/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-tech-writer
 displayName: Paige
 title: Technical Writer

src/bmm-skills/2-plan-workflows/bmad-agent-pm/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-pm
 displayName: John
 title: Product Manager

src/bmm-skills/2-plan-workflows/bmad-agent-ux-designer/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-ux-designer
 displayName: Sally
 title: UX Designer

src/bmm-skills/3-solutioning/bmad-agent-architect/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-architect
 displayName: Winston
 title: Architect

src/bmm-skills/4-implementation/bmad-agent-dev/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-dev
 displayName: Amelia
 title: Developer Agent

src/bmm-skills/4-implementation/bmad-agent-qa/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-qa
 displayName: Quinn
 title: QA Engineer

src/bmm-skills/4-implementation/bmad-agent-quick-flow-solo-dev/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-quick-flow-solo-dev
 displayName: Barry
 title: Quick Flow Solo Dev

src/bmm-skills/4-implementation/bmad-agent-sm/bmad-skill-manifest.yaml

@@ -1,4 +1,4 @@
-type: skill
+type: agent
 name: bmad-agent-sm
 displayName: Bob
 title: Scrum Master

tools/installer/core/installer.js

@@ -42,7 +42,7 @@ class Installer {
       const officialModules = await OfficialModules.build(config, paths);
       const existingInstall = await ExistingInstall.detect(paths.bmadDir);
 
-      await this.customModules.discoverPaths(config, paths);
+      await this.customModules.discoverPaths(customConfig, paths);
 
       if (existingInstall.installed) {
         await this._removeDeselectedModules(existingInstall, config, paths);

tools/installer/core/manifest-generator.js

@@ -268,64 +268,66 @@ class ManifestGenerator {
   }
 
   /**
-   * Collect all agents from core and selected modules
+   * Collect all agents from selected modules by walking their directory trees.
-   * Scans the INSTALLED bmad directory, not the source
    */
   async collectAgents(selectedModules) {
     this.agents = [];
+    const debug = process.env.BMAD_DEBUG_MANIFEST === 'true';
 
-    // Use updatedModules which already includes deduplicated 'core' + selectedModules
+    // Walk each module's full directory tree looking for type:agent manifests
     for (const moduleName of this.updatedModules) {
-      const agentsPath = path.join(this.bmadDir, moduleName, 'agents');
+      const modulePath = path.join(this.bmadDir, moduleName);
+      if (!(await fs.pathExists(modulePath))) continue;
 
-      if (await fs.pathExists(agentsPath)) {
+      const moduleAgents = await this.getAgentsFromDirRecursive(modulePath, moduleName, '', debug);
-        const moduleAgents = await this.getAgentsFromDir(agentsPath, moduleName);
       this.agents.push(...moduleAgents);
     }
-    }
 
     // Get standalone agents from bmad/agents/ directory
     const standaloneAgentsDir = path.join(this.bmadDir, 'agents');
     if (await fs.pathExists(standaloneAgentsDir)) {
-      const agentDirs = await fs.readdir(standaloneAgentsDir, { withFileTypes: true });
+      const standaloneAgents = await this.getAgentsFromDirRecursive(standaloneAgentsDir, 'standalone', '', debug);
-
-      for (const agentDir of agentDirs) {
-        if (!agentDir.isDirectory()) continue;
-
-        const agentDirPath = path.join(standaloneAgentsDir, agentDir.name);
-        const standaloneAgents = await this.getAgentsFromDir(agentDirPath, 'standalone');
       this.agents.push(...standaloneAgents);
     }
+
+    if (debug) {
+      console.log(`[DEBUG] collectAgents: total agents found: ${this.agents.length}`);
     }
   }
 
   /**
-   * Get agents from a directory recursively
+   * Recursively walk a directory tree collecting agents.
-   * Only includes .md files with agent content
+   * Discovers agents via directory with bmad-skill-manifest.yaml containing type: agent
+   *
+   * @param {string} dirPath - Current directory being scanned
+   * @param {string} moduleName - Module this directory belongs to
+   * @param {string} relativePath - Path relative to the module root (for install path construction)
+   * @param {boolean} debug - Emit debug messages
    */
-  async getAgentsFromDir(dirPath, moduleName, relativePath = '') {
+  async getAgentsFromDirRecursive(dirPath, moduleName, relativePath = '', debug = false) {
-    // Skip directories claimed by collectSkills
-    if (this.skillClaimedDirs && this.skillClaimedDirs.has(dirPath)) return [];
     const agents = [];
-    const entries = await fs.readdir(dirPath, { withFileTypes: true });
+    let entries;
-    // Load skill manifest for this directory (if present)
+    try {
-    const skillManifest = await this.loadSkillManifest(dirPath);
+      entries = await fs.readdir(dirPath, { withFileTypes: true });
+    } catch {
+      return agents;
+    }
 
     for (const entry of entries) {
+      if (!entry.isDirectory()) continue;
+      if (entry.name.startsWith('.') || entry.name.startsWith('_')) continue;
+
       const fullPath = path.join(dirPath, entry.name);
 
-      if (entry.isDirectory()) {
+      // Check for type:agent manifest BEFORE checking skillClaimedDirs —
-        // Check for new-format agent: bmad-skill-manifest.yaml with type: agent
+      // agent dirs may be claimed by collectSkills for IDE installation,
-        // Note: type:agent dirs may also be claimed by collectSkills for IDE installation,
+      // but we still need them in agent-manifest.csv.
-        // but we still need to process them here for agent-manifest.csv
       const dirManifest = await this.loadSkillManifest(fullPath);
       if (dirManifest && dirManifest.__single && dirManifest.__single.type === 'agent') {
         const m = dirManifest.__single;
         const dirRelativePath = relativePath ? `${relativePath}/${entry.name}` : entry.name;
-          const installPath =
+        const agentModule = m.module || moduleName;
-            moduleName === 'core'
+        const installPath = `${this.bmadFolderName}/${agentModule}/${dirRelativePath}`;
-              ? `${this.bmadFolderName}/core/agents/${dirRelativePath}`
-              : `${this.bmadFolderName}/${moduleName}/agents/${dirRelativePath}`;
 
         agents.push({
           name: m.name || entry.name,
@@ -337,7 +339,7 @@ class ManifestGenerator {
           identity: m.identity ? this.cleanForCSV(m.identity) : '',
           communicationStyle: m.communicationStyle ? this.cleanForCSV(m.communicationStyle) : '',
           principles: m.principles ? this.cleanForCSV(m.principles) : '',
-            module: m.module || moduleName,
+          module: agentModule,
           path: installPath,
           canonicalId: m.canonicalId || '',
         });
@@ -345,76 +347,24 @@ class ManifestGenerator {
         this.files.push({
           type: 'agent',
           name: m.name || entry.name,
-            module: moduleName,
+          module: agentModule,
           path: installPath,
         });
+
+        if (debug) {
+          console.log(`[DEBUG] collectAgents: found type:agent "${m.name || entry.name}" at ${fullPath}`);
+        }
         continue;
       }
 
-        // Skip directories claimed by collectSkills (non-agent type skills)
+      // Skip directories claimed by collectSkills (non-agent type skills) —
+      // avoids recursing into skill trees that can't contain agents.
       if (this.skillClaimedDirs && this.skillClaimedDirs.has(fullPath)) continue;
 
       // Recurse into subdirectories
       const newRelativePath = relativePath ? `${relativePath}/${entry.name}` : entry.name;
-        const subDirAgents = await this.getAgentsFromDir(fullPath, moduleName, newRelativePath);
+      const subDirAgents = await this.getAgentsFromDirRecursive(fullPath, moduleName, newRelativePath, debug);
       agents.push(...subDirAgents);
-      } else if (entry.name.endsWith('.md') && entry.name.toLowerCase() !== 'readme.md') {
-        const content = await fs.readFile(fullPath, 'utf8');
-
-        // Skip files that don't contain <agent> tag (e.g., README files)
-        if (!content.includes('<agent')) {
-          continue;
-        }
-
-        // Skip web-only agents
-        if (content.includes('localskip="true"')) {
-          continue;
-        }
-
-        // Extract agent metadata from the XML structure
-        const nameMatch = content.match(/name="([^"]+)"/);
-        const titleMatch = content.match(/title="([^"]+)"/);
-        const iconMatch = content.match(/icon="([^"]+)"/);
-        const capabilitiesMatch = content.match(/capabilities="([^"]+)"/);
-
-        // Extract persona fields
-        const roleMatch = content.match(/<role>([^<]+)<\/role>/);
-        const identityMatch = content.match(/<identity>([\s\S]*?)<\/identity>/);
-        const styleMatch = content.match(/<communication_style>([\s\S]*?)<\/communication_style>/);
-        const principlesMatch = content.match(/<principles>([\s\S]*?)<\/principles>/);
-
-        // Build relative path for installation
-        const fileRelativePath = relativePath ? `${relativePath}/${entry.name}` : entry.name;
-        const installPath =
-          moduleName === 'core'
-            ? `${this.bmadFolderName}/core/agents/${fileRelativePath}`
-            : `${this.bmadFolderName}/${moduleName}/agents/${fileRelativePath}`;
-
-        const agentName = entry.name.replace('.md', '');
-
-        agents.push({
-          name: agentName,
-          displayName: nameMatch ? nameMatch[1] : agentName,
-          title: titleMatch ? titleMatch[1] : '',
-          icon: iconMatch ? iconMatch[1] : '',
-          capabilities: capabilitiesMatch ? this.cleanForCSV(capabilitiesMatch[1]) : '',
-          role: roleMatch ? this.cleanForCSV(roleMatch[1]) : '',
-          identity: identityMatch ? this.cleanForCSV(identityMatch[1]) : '',
-          communicationStyle: styleMatch ? this.cleanForCSV(styleMatch[1]) : '',
-          principles: principlesMatch ? this.cleanForCSV(principlesMatch[1]) : '',
-          module: moduleName,
-          path: installPath,
-          canonicalId: this.getCanonicalId(skillManifest, entry.name),
-        });
-
-        // Add to files list
-        this.files.push({
-          type: 'agent',
-          name: agentName,
-          module: moduleName,
-          path: installPath,
-        });
-      }
     }
 
     return agents;
@@ -704,21 +654,12 @@ class ManifestGenerator {
           continue;
         }
 
-        // Check if this looks like a module (has agents, workflows, or tasks directory)
+        // Check if this looks like a module (has agents directory or skill manifests)
         const modulePath = path.join(bmadDir, entry.name);
         const hasAgents = await fs.pathExists(path.join(modulePath, 'agents'));
-        const hasWorkflows = await fs.pathExists(path.join(modulePath, 'workflows'));
+        const hasSkills = await this._hasSkillMdRecursive(modulePath);
-        const hasTasks = await fs.pathExists(path.join(modulePath, 'tasks'));
-        const hasTools = await fs.pathExists(path.join(modulePath, 'tools'));
 
-        // Check for native-entrypoint-only modules: recursive scan for SKILL.md
+        if (hasAgents || hasSkills) {
-        let hasSkills = false;
-        if (!hasAgents && !hasWorkflows && !hasTasks && !hasTools) {
-          hasSkills = await this._hasSkillMdRecursive(modulePath);
-        }
-
-        // If it has any of these directories or skill manifests, it's likely a module
-        if (hasAgents || hasWorkflows || hasTasks || hasTools || hasSkills) {
           modules.push(entry.name);
         }
       }

tools/installer/ide/shared/bmad-artifacts.js

@@ -5,6 +5,33 @@ const { loadSkillManifest, getCanonicalId } = require('./skill-manifest');
 /**
  * Helpers for gathering BMAD agents/tasks from the installed tree.
  * Shared by installers that need Claude-style exports.
+ *
+ * TODO: Dead code cleanup — compiled XML agents are retired.
+ *
+ * All agents now use the SKILL.md directory format with bmad-skill-manifest.yaml
+ * (type: agent). The legacy pipeline below only discovers compiled .md files
+ * containing <agent> XML tags, which no longer exist. The following are dead:
+ *
+ *   - getAgentsFromBmad()      — scans {module}/agents/ for .md files with <agent> tags
+ *   - getAgentsFromDir()       — recursive helper for the above
+ *   - AgentCommandGenerator    — (agent-command-generator.js) generates launcher .md files
+ *                                 that tell the LLM to load a compiled agent .md file
+ *   - agent-command-template.md — (templates/) the launcher template with hardcoded
+ *                                 {module}/agents/{{path}} reference
+ *
+ * Agent metadata for agent-manifest.csv is now handled entirely by
+ * ManifestGenerator.getAgentsFromDirRecursive() in manifest-generator.js,
+ * which walks the full module tree and finds type:agent directories.
+ *
+ * IDE installation of agents is handled by the native skill pipeline —
+ * each agent's SKILL.md directory is installed directly to the IDE's
+ * skills path, so no launcher intermediary is needed.
+ *
+ * Cleanup: remove getAgentsFromBmad, getAgentsFromDir, their exports,
+ * AgentCommandGenerator, agent-command-template.md, and all call sites
+ * in IDE installers that invoke collectAgentArtifacts / writeAgentLaunchers /
+ * writeColonArtifacts / writeDashArtifacts.
+ * getTasksFromBmad and getTasksFromDir may still be live — verify before removing.
  */
 async function getAgentsFromBmad(bmadDir, selectedModules = []) {
   const agents = [];

tools/installer/ide/shared/skill-manifest.js

@@ -27,7 +27,7 @@ async function loadSkillManifest(dirPath) {
 /**
  * Get the canonicalId for a specific file from a loaded skill manifest.
  * @param {Object|null} manifest - Loaded manifest (from loadSkillManifest)
- * @param {string} filename - Source filename to look up (e.g., 'pm.md', 'help.md', 'pm.agent.yaml')
+ * @param {string} filename - Source filename to look up (e.g., 'pm.md', 'help.md')
  * @returns {string} canonicalId or empty string
  */
 function getCanonicalId(manifest, filename) {
@@ -36,12 +36,6 @@ function getCanonicalId(manifest, filename) {
   if (manifest.__single) return manifest.__single.canonicalId || '';
   // Multi-entry: look up by filename directly
   if (manifest[filename]) return manifest[filename].canonicalId || '';
-  // Fallback: try alternate extensions for compiled files
-  const baseName = filename.replace(/\.(md|xml)$/i, '');
-  const agentKey = `${baseName}.agent.yaml`;
-  if (manifest[agentKey]) return manifest[agentKey].canonicalId || '';
-  const xmlKey = `${baseName}.xml`;
-  if (manifest[xmlKey]) return manifest[xmlKey].canonicalId || '';
   return '';
 }
 
@@ -57,12 +51,6 @@ function getArtifactType(manifest, filename) {
   if (manifest.__single) return manifest.__single.type || null;
   // Multi-entry: look up by filename directly
   if (manifest[filename]) return manifest[filename].type || null;
-  // Fallback: try alternate extensions for compiled files
-  const baseName = filename.replace(/\.(md|xml)$/i, '');
-  const agentKey = `${baseName}.agent.yaml`;
-  if (manifest[agentKey]) return manifest[agentKey].type || null;
-  const xmlKey = `${baseName}.xml`;
-  if (manifest[xmlKey]) return manifest[xmlKey].type || null;
   return null;
 }
 
@@ -78,12 +66,6 @@ function getInstallToBmad(manifest, filename) {
   if (manifest.__single) return manifest.__single.install_to_bmad !== false;
   // Multi-entry: look up by filename directly
   if (manifest[filename]) return manifest[filename].install_to_bmad !== false;
-  // Fallback: try alternate extensions for compiled files
-  const baseName = filename.replace(/\.(md|xml)$/i, '');
-  const agentKey = `${baseName}.agent.yaml`;
-  if (manifest[agentKey]) return manifest[agentKey].install_to_bmad !== false;
-  const xmlKey = `${baseName}.xml`;
-  if (manifest[xmlKey]) return manifest[xmlKey].install_to_bmad !== false;
   return true;
 }
 

tools/installer/modules/official-modules.js

@@ -1624,8 +1624,49 @@ class OfficialModules {
         return match;
       }
 
+      const configValue = this.resolveConfigValue(configKey, currentModule, moduleConfig);
+
+      return configValue || match;
+    });
+  }
+
+  /**
+   * Clean a stored path-like value for prompt display/input reuse.
+   * @param {*} value - Stored value
+   * @returns {*} Cleaned value
+   */
+  cleanPromptValue(value) {
+    if (typeof value === 'string' && value.startsWith('{project-root}/')) {
+      return value.replace('{project-root}/', '');
+    }
+
+    return value;
+  }
+
+  /**
+   * Resolve a config key from answers, collected config, existing config, or schema defaults.
+   * @param {string} configKey - Config key to resolve
+   * @param {string} currentModule - Current module name
+   * @param {Object} moduleConfig - Current module config schema
+   * @returns {*} Resolved value
+   */
+  resolveConfigValue(configKey, currentModule = null, moduleConfig = null) {
     // Look for the config value in allAnswers (already answered questions)
-      let configValue = this.allAnswers[configKey] || this.allAnswers[`core_${configKey}`];
+    let configValue = this.allAnswers?.[configKey] || this.allAnswers?.[`core_${configKey}`];
+
+    if (!configValue && this.allAnswers) {
+      for (const [answerKey, answerValue] of Object.entries(this.allAnswers)) {
+        if (answerKey.endsWith(`_${configKey}`)) {
+          configValue = answerValue;
+          break;
+        }
+      }
+    }
+
+    // Prefer the current module's persisted value when re-prompting an existing install
+    if (!configValue && currentModule && this._existingConfig?.[currentModule]?.[configKey] !== undefined) {
+      configValue = this._existingConfig[currentModule][configKey];
+    }
 
     // Check in already collected config
     if (!configValue) {
@@ -1637,6 +1678,16 @@ class OfficialModules {
       }
     }
 
+    // Fall back to other existing module config values
+    if (!configValue && this._existingConfig) {
+      for (const mod of Object.keys(this._existingConfig)) {
+        if (mod !== '_meta' && this._existingConfig[mod] && this._existingConfig[mod][configKey]) {
+          configValue = this._existingConfig[mod][configKey];
+          break;
+        }
+      }
+    }
+
     // If still not found and we're in the same module, use the default from the config schema
     if (!configValue && currentModule && moduleConfig && moduleConfig[configKey]) {
       const referencedItem = moduleConfig[configKey];
@@ -1645,8 +1696,49 @@ class OfficialModules {
       }
     }
 
-      return configValue || match;
+    return this.cleanPromptValue(configValue);
-    });
+  }
+
+  /**
+   * Convert an existing stored value back into the prompt-facing value for templated fields.
+   * For example, "{test_artifacts}/{value}" + "_bmad-output/test-artifacts/test-design"
+   * becomes "test-design" so the template is not applied twice on modify.
+   * @param {*} existingValue - Stored config value
+   * @param {string} moduleName - Module name
+   * @param {Object} item - Config item definition
+   * @param {Object} moduleConfig - Current module config schema
+   * @returns {*} Prompt-facing default value
+   */
+  normalizeExistingValueForPrompt(existingValue, moduleName, item, moduleConfig = null) {
+    const cleanedValue = this.cleanPromptValue(existingValue);
+
+    if (typeof cleanedValue !== 'string' || typeof item?.result !== 'string' || !item.result.includes('{value}')) {
+      return cleanedValue;
+    }
+
+    const [prefixTemplate = '', suffixTemplate = ''] = item.result.split('{value}');
+    const prefix = this.cleanPromptValue(this.replacePlaceholders(prefixTemplate, moduleName, moduleConfig));
+    const suffix = this.cleanPromptValue(this.replacePlaceholders(suffixTemplate, moduleName, moduleConfig));
+
+    if ((prefix && !cleanedValue.startsWith(prefix)) || (suffix && !cleanedValue.endsWith(suffix))) {
+      return cleanedValue;
+    }
+
+    const startIndex = prefix.length;
+    const endIndex = suffix ? cleanedValue.length - suffix.length : cleanedValue.length;
+    if (endIndex < startIndex) {
+      return cleanedValue;
+    }
+
+    let promptValue = cleanedValue.slice(startIndex, endIndex);
+    if (promptValue.startsWith('/')) {
+      promptValue = promptValue.slice(1);
+    }
+    if (promptValue.endsWith('/')) {
+      promptValue = promptValue.slice(0, -1);
+    }
+
+    return promptValue || cleanedValue;
   }
 
   /**
@@ -1663,12 +1755,7 @@ class OfficialModules {
     let existingValue = null;
     if (this._existingConfig && this._existingConfig[moduleName]) {
       existingValue = this._existingConfig[moduleName][key];
-
+      existingValue = this.normalizeExistingValueForPrompt(existingValue, moduleName, item, moduleConfig);
-      // Clean up existing value - remove {project-root}/ prefix if present
-      // This prevents duplication when the result template adds it back
-      if (typeof existingValue === 'string' && existingValue.startsWith('{project-root}/')) {
-        existingValue = existingValue.replace('{project-root}/', '');
-      }
     }
 
     // Special handling for user_name: default to system user