fixed issue with agent customization application, now all fields are customized form the custom yaml. also added a recompile agents menu item

package-lock.json

@@ -1,12 +1,12 @@
 {
   "name": "bmad-method",
-  "version": "6.0.0-alpha.16",
+  "version": "6.0.0-alpha.17",
   "lockfileVersion": 3,
   "requires": true,
   "packages": {
     "": {
       "name": "bmad-method",
-      "version": "6.0.0-alpha.16",
+      "version": "6.0.0-alpha.17",
       "license": "MIT",
       "dependencies": {
         "@kayvan/markdown-tree-parser": "^1.6.1",

tools/cli/commands/install.js

@@ -35,6 +35,15 @@ module.exports = {
         return;
       }
 
+      // Handle compile agents separately
+      if (config.actionType === 'compile-agents') {
+        const result = await installer.compileAgents(config);
+        console.log(chalk.green('\n✨ Agent recompilation complete!'));
+        console.log(chalk.cyan(`Recompiled ${result.agentCount} agents with customizations applied`));
+        process.exit(0);
+        return;
+      }
+
       // Regular install/update flow
       const result = await installer.install(config);
 

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

@@ -229,7 +229,7 @@ class Installer {
         If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
          - Use Bash tool: \`.claude/hooks/bmad-speak.sh '[Agent Name]' '[dialogue]'\`
          - This speaks the dialogue with the agent's unique voice
-         - Run in background (&) to not block next agent`,
+         - Run in background to not block next agent`,
       );
 
       // Replace agent-tts injection marker with TTS rule for individual agents
@@ -2082,108 +2082,6 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
     }
   }
 
-  /**
-   * Compile/rebuild all agents and tasks for quick updates
-   * @param {Object} config - Compilation configuration
-   * @returns {Object} Compilation results
-   */
-  async compileAgents(config) {
-    try {
-      const projectDir = path.resolve(config.directory);
-      const { bmadDir } = await this.findBmadDir(projectDir);
-
-      // Check if bmad directory exists
-      if (!(await fs.pathExists(bmadDir))) {
-        throw new Error(`BMAD not installed at ${bmadDir}`);
-      }
-
-      // Get installed modules from manifest
-      const manifestPath = path.join(bmadDir, '_config', 'manifest.yaml');
-      let installedModules = [];
-      let manifest = null;
-      if (await fs.pathExists(manifestPath)) {
-        const manifestContent = await fs.readFile(manifestPath, 'utf8');
-        const yaml = require('yaml');
-        manifest = yaml.parse(manifestContent);
-        installedModules = manifest.modules || [];
-      }
-
-      // Check for custom modules with missing sources
-      if (manifest && manifest.customModules && manifest.customModules.length > 0) {
-        console.log(chalk.yellow('\nChecking custom module sources before compilation...'));
-
-        const customModuleSources = new Map();
-        for (const customModule of manifest.customModules) {
-          customModuleSources.set(customModule.id, customModule);
-        }
-
-        const projectRoot = getProjectRoot();
-        await this.handleMissingCustomSources(customModuleSources, bmadDir, projectRoot, 'compile-agents', installedModules);
-      }
-
-      let agentCount = 0;
-      let taskCount = 0;
-
-      // Process all modules in bmad directory
-      const entries = await fs.readdir(bmadDir, { withFileTypes: true });
-
-      for (const entry of entries) {
-        if (entry.isDirectory() && entry.name !== '_config' && entry.name !== 'docs') {
-          const modulePath = path.join(bmadDir, entry.name);
-
-          // Special handling for standalone agents in bmad/agents/ directory
-          if (entry.name === 'agents') {
-            await this.buildStandaloneAgents(bmadDir, projectDir);
-
-            // Count standalone agents
-            const standaloneAgentsPath = path.join(bmadDir, 'agents');
-            const standaloneAgentDirs = await fs.readdir(standaloneAgentsPath, { withFileTypes: true });
-            for (const agentDir of standaloneAgentDirs) {
-              if (agentDir.isDirectory()) {
-                const agentDirPath = path.join(standaloneAgentsPath, agentDir.name);
-                const agentFiles = await fs.readdir(agentDirPath);
-                agentCount += agentFiles.filter((f) => f.endsWith('.md') && !f.endsWith('.agent.yaml')).length;
-              }
-            }
-          } else {
-            // Rebuild module agents from installer source
-            const agentsPath = path.join(modulePath, 'agents');
-            if (await fs.pathExists(agentsPath)) {
-              await this.rebuildAgentFiles(modulePath, entry.name);
-              const agentFiles = await fs.readdir(agentsPath);
-              agentCount += agentFiles.filter((f) => f.endsWith('.md')).length;
-            }
-
-            // Count tasks (already built)
-            const tasksPath = path.join(modulePath, 'tasks');
-            if (await fs.pathExists(tasksPath)) {
-              const taskFiles = await fs.readdir(tasksPath);
-              taskCount += taskFiles.filter((f) => f.endsWith('.md')).length;
-            }
-          }
-        }
-      }
-
-      // Update IDE configurations using the existing IDE list from manifest
-      if (manifest && manifest.ides && manifest.ides.length > 0) {
-        for (const ide of manifest.ides) {
-          await this.ideManager.setup(ide, projectDir, bmadDir, {
-            selectedModules: installedModules,
-            skipModuleInstall: true, // Skip module installation, just update IDE files
-            verbose: config.verbose,
-            preCollectedConfig: { _alreadyConfigured: true }, // Skip all interactive prompts during compile
-          });
-        }
-        console.log(chalk.green('✓ IDE configurations updated'));
-      } else {
-        console.log(chalk.yellow('⚠️  No IDEs configured. Skipping IDE update.'));
-      }
-      return { agentCount, taskCount };
-    } catch (error) {
-      throw error;
-    }
-  }
-
   /**
    * Private: Update core
    */
@@ -2404,6 +2302,108 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
     }
   }
 
+  /**
+   * Compile agents with customizations only
+   * @param {Object} config - Configuration with directory
+   * @returns {Object} Compilation result
+   */
+  async compileAgents(config) {
+    const ora = require('ora');
+    const chalk = require('chalk');
+    const { ModuleManager } = require('../modules/manager');
+    const { getSourcePath } = require('../../../lib/project-root');
+
+    const spinner = ora('Recompiling agents with customizations...').start();
+
+    try {
+      const projectDir = path.resolve(config.directory);
+      const { bmadDir } = await this.findBmadDir(projectDir);
+
+      // Check if bmad directory exists
+      if (!(await fs.pathExists(bmadDir))) {
+        spinner.fail('No BMAD installation found');
+        throw new Error(`BMAD not installed at ${bmadDir}. Use regular install for first-time setup.`);
+      }
+
+      // Detect existing installation
+      const existingInstall = await this.detector.detect(bmadDir);
+      const installedModules = existingInstall.modules.map((m) => m.id);
+
+      // Initialize module manager
+      const moduleManager = new ModuleManager();
+      moduleManager.setBmadFolderName(path.basename(bmadDir));
+
+      let totalAgentCount = 0;
+
+      // Get custom module sources from cache
+      const customModuleSources = new Map();
+      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);
+            const moduleYamlPath = path.join(cachedPath, 'module.yaml');
+
+            // Check if this is actually a custom module
+            if (await fs.pathExists(moduleYamlPath)) {
+              customModuleSources.set(moduleId, cachedPath);
+            }
+          }
+        }
+      }
+
+      // Process each installed module
+      for (const moduleId of installedModules) {
+        spinner.text = `Recompiling agents in ${moduleId}...`;
+
+        // Get source path
+        let sourcePath;
+        if (moduleId === 'core') {
+          sourcePath = getSourcePath('core');
+        } else {
+          // First check if it's in the custom cache
+          if (customModuleSources.has(moduleId)) {
+            sourcePath = customModuleSources.get(moduleId);
+          } else {
+            sourcePath = await moduleManager.findModuleSource(moduleId);
+          }
+        }
+
+        if (!sourcePath) {
+          console.log(chalk.yellow(`  Warning: Source not found for module ${moduleId}, skipping...`));
+          continue;
+        }
+
+        const targetPath = path.join(bmadDir, moduleId);
+
+        // Compile agents for this module
+        await moduleManager.compileModuleAgents(sourcePath, targetPath, moduleId, bmadDir, this);
+
+        // Count agents (rough estimate based on files)
+        const agentsPath = path.join(targetPath, 'agents');
+        if (await fs.pathExists(agentsPath)) {
+          const agentFiles = await fs.readdir(agentsPath);
+          const agentCount = agentFiles.filter((f) => f.endsWith('.md')).length;
+          totalAgentCount += agentCount;
+        }
+      }
+
+      spinner.succeed('Agent recompilation complete!');
+
+      return {
+        success: true,
+        agentCount: totalAgentCount,
+        modules: installedModules,
+      };
+    } catch (error) {
+      spinner.fail('Agent recompilation failed');
+      throw error;
+    }
+  }
+
   /**
    * Private: Prompt for update action
    */

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

@@ -731,7 +731,7 @@ class ModuleManager {
   async compileModuleAgents(sourcePath, targetPath, moduleName, bmadDir, installer = null) {
     const sourceAgentsPath = path.join(sourcePath, 'agents');
     const targetAgentsPath = path.join(targetPath, 'agents');
-    const cfgAgentsDir = path.join(bmadDir, '_config', 'agents');
+    const cfgAgentsDir = path.join(bmadDir, '_bmad', '_config', 'agents');
 
     // Check if agents directory exists in source
     if (!(await fs.pathExists(sourceAgentsPath))) {
@@ -809,9 +809,9 @@ class ModuleManager {
           const customizeData = yaml.parse(customizeContent);
           customizedFields = customizeData.customized_fields || [];
 
-          // Build answers object from customizations (filter empty values)
+          // Build answers object from customizations
           if (customizeData.persona) {
-            Object.assign(answers, filterCustomizationData(customizeData.persona));
+            answers.persona = customizeData.persona;
           }
           if (customizeData.agent?.metadata) {
             const filteredMetadata = filterCustomizationData(customizeData.agent.metadata);
@@ -825,6 +825,12 @@ class ModuleManager {
           if (customizeData.memories && customizeData.memories.length > 0) {
             answers.memories = customizeData.memories;
           }
+          if (customizeData.menu && customizeData.menu.length > 0) {
+            answers.menu = customizeData.menu;
+          }
+          if (customizeData.prompts && customizeData.prompts.length > 0) {
+            answers.prompts = customizeData.prompts;
+          }
         }
 
         // Check if agent has sidecar
@@ -839,8 +845,14 @@ class ModuleManager {
         // Compile with customizations if any
         const { xml } = await compileAgent(yamlContent, answers, agentName, relativePath, { config: this.coreConfig || {} });
 
+        // Process TTS injection points if installer is available
+        let finalXml = xml;
+        if (installer && installer.processTTSInjectionPoints) {
+          finalXml = installer.processTTSInjectionPoints(xml, targetMdPath);
+        }
+
         // Write the compiled agent
-        await fs.writeFile(targetMdPath, xml, 'utf8');
+        await fs.writeFile(targetMdPath, finalXml, 'utf8');
 
         // Handle sidecar copying if present
         if (hasSidecar) {

tools/cli/lib/agent/compiler.js

@@ -98,6 +98,25 @@ function buildPromptsXml(prompts) {
   return xml;
 }
 
+/**
+ * Build memories XML section
+ * @param {Array} memories - Memories array
+ * @returns {string} Memories XML
+ */
+function buildMemoriesXml(memories) {
+  if (!memories || memories.length === 0) return '';
+
+  let xml = '  <memories>\n';
+
+  for (const memory of memories) {
+    xml += `    <memory>${escapeXml(String(memory))}</memory>\n`;
+  }
+
+  xml += '  </memories>\n';
+
+  return xml;
+}
+
 /**
  * Build menu XML section
  * Supports both legacy and multi format menu items
@@ -285,6 +304,11 @@ async function compileToXml(agentYaml, agentName = '', targetPath = '') {
     xml += buildPromptsXml(agent.prompts);
   }
 
+  // Memories section (if present)
+  if (agent.memories && agent.memories.length > 0) {
+    xml += buildMemoriesXml(agent.memories);
+  }
+
   // Menu section
   xml += buildMenuXml(agent.menu || []);
 
@@ -323,6 +347,80 @@ async function compileAgent(yamlContent, answers = {}, agentName = '', targetPat
     answers = templateAnswers;
   }
 
+  // Handle other customization properties
+  // These should be merged into the agent structure, not processed as template variables
+  const customizationKeys = ['persona', 'critical_actions', 'memories', 'menu', 'prompts'];
+  const customizations = {};
+  const remainingAnswers = { ...answers };
+
+  for (const key of customizationKeys) {
+    if (answers[key]) {
+      let filtered;
+
+      // Handle different data types
+      if (Array.isArray(answers[key])) {
+        // For arrays, filter out empty/null/undefined values
+        filtered = answers[key].filter((item) => item !== null && item !== undefined && item !== '');
+      } else {
+        // For objects, use filterCustomizationData
+        filtered = filterCustomizationData(answers[key]);
+      }
+
+      // Check if we have valid content
+      const hasContent = Array.isArray(filtered) ? filtered.length > 0 : Object.keys(filtered).length > 0;
+
+      if (hasContent) {
+        customizations[key] = filtered;
+      }
+      delete remainingAnswers[key];
+    }
+  }
+
+  // Merge customizations into agentYaml
+  if (Object.keys(customizations).length > 0) {
+    // For persona: replace entire section
+    if (customizations.persona) {
+      agentYaml.agent.persona = customizations.persona;
+    }
+
+    // For critical_actions: append to existing or create new
+    if (customizations.critical_actions) {
+      const existing = agentYaml.agent.critical_actions || [];
+      agentYaml.agent.critical_actions = [...existing, ...customizations.critical_actions];
+    }
+
+    // For memories: append to existing or create new
+    if (customizations.memories) {
+      const existing = agentYaml.agent.memories || [];
+      agentYaml.agent.memories = [...existing, ...customizations.memories];
+    }
+
+    // For menu: append to existing or create new
+    if (customizations.menu) {
+      const existing = agentYaml.agent.menu || [];
+      agentYaml.agent.menu = [...existing, ...customizations.menu];
+    }
+
+    // For prompts: append to existing or create new (by id)
+    if (customizations.prompts) {
+      const existing = agentYaml.agent.prompts || [];
+      // Merge by id, with customizations taking precedence
+      const mergedPrompts = [...existing];
+      for (const customPrompt of customizations.prompts) {
+        const existingIndex = mergedPrompts.findIndex((p) => p.id === customPrompt.id);
+        if (existingIndex === -1) {
+          mergedPrompts.push(customPrompt);
+        } else {
+          mergedPrompts[existingIndex] = customPrompt;
+        }
+      }
+      agentYaml.agent.prompts = mergedPrompts;
+    }
+  }
+
+  // Use remaining answers for template processing
+  answers = remainingAnswers;
+
   // Extract install_config
   const installConfig = extractInstallConfig(agentYaml);
 
@@ -460,6 +558,7 @@ module.exports = {
   buildFrontmatter,
   buildPersonaXml,
   buildPromptsXml,
+  buildMemoriesXml,
   buildMenuXml,
   filterCustomizationData,
 };

tools/cli/lib/ui.js

@@ -189,6 +189,14 @@ class UI {
         });
       }
 
+      // Add custom agent compilation option
+      if (installedVersion !== 'unknown') {
+        choices.push({
+          name: 'Recompile Agents (apply customizations only)',
+          value: 'compile-agents',
+        });
+      }
+
       // Common actions
       choices.push({ name: 'Modify BMAD Installation', value: 'update' });
 
@@ -215,6 +223,16 @@ class UI {
         };
       }
 
+      // Handle compile agents separately
+      if (actionType === 'compile-agents') {
+        // Only recompile agents with customizations, don't update any files
+        return {
+          actionType: 'compile-agents',
+          directory: confirmedDirectory,
+          customContent: { hasCustomContent: false },
+        };
+      }
+
       // If actionType === 'update', handle it with the new flow
       // Return early with modify configuration
       if (actionType === 'update') {