diff --git a/src/modules/bmm/testarch/knowledge/overview.md b/src/modules/bmm/testarch/knowledge/overview.md
index 5fbb9801..8155d55f 100644
--- a/src/modules/bmm/testarch/knowledge/overview.md
+++ b/src/modules/bmm/testarch/knowledge/overview.md
@@ -31,7 +31,6 @@ npm install -D @seontechnologies/playwright-utils
 
 - `@playwright/test` >= 1.54.1 (required)
 - `ajv` >= 8.0.0 (optional - for JSON Schema validation)
-- `js-yaml` >= 4.0.0 (optional - for YAML schema support)
 - `zod` >= 3.0.0 (optional - for Zod schema validation)
 
 ## Available Utilities
diff --git a/test/README.md b/test/README.md
index 6253bd7e..da2f2962 100644
--- a/test/README.md
+++ b/test/README.md
@@ -269,7 +269,7 @@ The validation is integrated into the GitHub Actions workflow:
 ## Dependencies
 
 - **zod**: Schema validation library
-- **js-yaml**: YAML parsing
+- **yaml**: YAML parsing
 - **glob**: File pattern matching
 - **c8**: Code coverage reporting
 
diff --git a/test/test-agent-schema.js b/test/test-agent-schema.js
index 51cd65bb..ecb3b673 100644
--- a/test/test-agent-schema.js
+++ b/test/test-agent-schema.js
@@ -10,7 +10,7 @@
 
 const fs = require('node:fs');
 const path = require('node:path');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { validateAgentFile } = require('../tools/schema/agent.js');
 const { glob } = require('glob');
 
@@ -182,7 +182,7 @@ function runTest(filePath) {
     let agentData;
 
     try {
-      agentData = yaml.load(fileContent);
+      agentData = yaml.parse(fileContent);
     } catch (parseError) {
       // YAML parse error
       if (shouldPass) {
diff --git a/tools/cli/installers/lib/core/config-collector.js b/tools/cli/installers/lib/core/config-collector.js
index 8f0c9885..d82e345f 100644
--- a/tools/cli/installers/lib/core/config-collector.js
+++ b/tools/cli/installers/lib/core/config-collector.js
@@ -1,6 +1,6 @@
 const path = require('node:path');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const chalk = require('chalk');
 const inquirer = require('inquirer');
 const { getProjectRoot, getModulePath } = require('../../../lib/project-root');
@@ -109,7 +109,7 @@ class ConfigCollector {
         if (await fs.pathExists(moduleConfigPath)) {
           try {
             const content = await fs.readFile(moduleConfigPath, 'utf8');
-            const moduleConfig = yaml.load(content);
+            const moduleConfig = yaml.parse(content);
             if (moduleConfig) {
               this.existingConfig[entry.name] = moduleConfig;
               foundAny = true;
@@ -238,7 +238,7 @@ class ConfigCollector {
     }
 
     const configContent = await fs.readFile(configPath, 'utf8');
-    const moduleConfig = yaml.load(configContent);
+    const moduleConfig = yaml.parse(configContent);
 
     if (!moduleConfig) {
       return false;
@@ -514,7 +514,7 @@ class ConfigCollector {
     }
 
     const configContent = await fs.readFile(configPath, 'utf8');
-    const moduleConfig = yaml.load(configContent);
+    const moduleConfig = yaml.parse(configContent);
 
     if (!moduleConfig) {
       return;
diff --git a/tools/cli/installers/lib/core/custom-module-cache.js b/tools/cli/installers/lib/core/custom-module-cache.js
index 0261efc7..a3945039 100644
--- a/tools/cli/installers/lib/core/custom-module-cache.js
+++ b/tools/cli/installers/lib/core/custom-module-cache.js
@@ -31,7 +31,7 @@ class CustomModuleCache {
     }
 
     const content = await fs.readFile(this.manifestPath, 'utf8');
-    const yaml = require('js-yaml');
+    const yaml = require('yaml');
     return yaml.parse(content) || {};
   }
 
@@ -39,11 +39,10 @@ class CustomModuleCache {
    * Update cache manifest
    */
   async updateCacheManifest(manifest) {
-    const yaml = require('js-yaml');
-    const content = yaml.dump(manifest, {
+    const yaml = require('yaml');
+    const content = yaml.stringify(manifest, {
       indent: 2,
-      lineWidth: -1,
-      noRefs: true,
+      lineWidth: 0,
       sortKeys: false,
     });
 
diff --git a/tools/cli/installers/lib/core/dependency-resolver.js b/tools/cli/installers/lib/core/dependency-resolver.js
index c53aec58..7ed4716f 100644
--- a/tools/cli/installers/lib/core/dependency-resolver.js
+++ b/tools/cli/installers/lib/core/dependency-resolver.js
@@ -2,7 +2,7 @@ const fs = require('fs-extra');
 const path = require('node:path');
 const glob = require('glob');
 const chalk = require('chalk');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 
 /**
  * Dependency Resolver for BMAD modules
@@ -147,7 +147,7 @@ class DependencyResolver {
           // Quote values with backticks to make them valid YAML
           yamlContent = yamlContent.replaceAll(/: `([^`]+)`/g, ': "$1"');
 
-          const frontmatter = yaml.load(yamlContent);
+          const frontmatter = yaml.parse(yamlContent);
           if (frontmatter.dependencies) {
             const deps = Array.isArray(frontmatter.dependencies) ? frontmatter.dependencies : [frontmatter.dependencies];
 
diff --git a/tools/cli/installers/lib/core/detector.js b/tools/cli/installers/lib/core/detector.js
index 251b60f5..f87034e0 100644
--- a/tools/cli/installers/lib/core/detector.js
+++ b/tools/cli/installers/lib/core/detector.js
@@ -1,6 +1,6 @@
 const path = require('node:path');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { Manifest } = require('./manifest');
 
 class Detector {
@@ -237,7 +237,7 @@ class Detector {
         return false;
       }
       try {
-        const yaml = require('js-yaml');
+        const yaml = require('yaml');
         const manifestContent = await fs.readFile(manifestPath, 'utf8');
         const manifest = yaml.parse(manifestContent);
         // V6+ manifest has installation.version
diff --git a/tools/cli/installers/lib/core/ide-config-manager.js b/tools/cli/installers/lib/core/ide-config-manager.js
index 8b09a8c2..91ca2b79 100644
--- a/tools/cli/installers/lib/core/ide-config-manager.js
+++ b/tools/cli/installers/lib/core/ide-config-manager.js
@@ -1,6 +1,6 @@
 const path = require('node:path');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 
 /**
  * Manages IDE configuration persistence
@@ -61,10 +61,9 @@ class IdeConfigManager {
       configuration: configuration || {},
     };
 
-    const yamlContent = yaml.dump(configData, {
+    const yamlContent = yaml.stringify(configData, {
       indent: 2,
-      lineWidth: -1,
-      noRefs: true,
+      lineWidth: 0,
       sortKeys: false,
     });
 
@@ -88,7 +87,7 @@ class IdeConfigManager {
 
     try {
       const content = await fs.readFile(configPath, 'utf8');
-      const config = yaml.load(content);
+      const config = yaml.parse(content);
       return config;
     } catch (error) {
       console.warn(`Warning: Failed to load IDE config for ${ideName}:`, error.message);
diff --git a/tools/cli/installers/lib/core/installer.js b/tools/cli/installers/lib/core/installer.js
index 4a70e1ed..77ec343c 100644
--- a/tools/cli/installers/lib/core/installer.js
+++ b/tools/cli/installers/lib/core/installer.js
@@ -18,6 +18,7 @@ const { CLIUtils } = require('../../../lib/cli-utils');
 const { ManifestGenerator } = require('./manifest-generator');
 const { IdeConfigManager } = require('./ide-config-manager');
 const { CustomHandler } = require('../custom/handler');
+const { filterCustomizationData } = require('../../../lib/agent/compiler');
 
 class Installer {
   constructor() {
@@ -1457,7 +1458,7 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
    * @param {Object} moduleConfigs - Collected configuration values
    */
   async generateModuleConfigs(bmadDir, moduleConfigs) {
-    const yaml = require('js-yaml');
+    const yaml = require('yaml');
 
     // Extract core config values to share with other modules
     const coreConfig = moduleConfigs.core || {};
@@ -1504,11 +1505,10 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
         }
 
         // Convert config to YAML
-        let yamlContent = yaml.dump(finalConfig, {
+        let yamlContent = yaml.stringify(finalConfig, {
           indent: 2,
-          lineWidth: -1,
-          noRefs: true,
-          sortKeys: false,
+          lineWidth: 0,
+          minContentWidth: 0,
         });
 
         // If we have core values, reorganize the YAML to group them with their comment
@@ -1949,7 +1949,7 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
 
       if (customizeExists) {
         const customizeContent = await fs.readFile(customizePath, 'utf8');
-        const yaml = require('js-yaml');
+        const yaml = require('yaml');
         const customizeYaml = yaml.parse(customizeContent);
 
         // Detect what fields are customized (similar to rebuildAgentFiles)
@@ -2040,8 +2040,8 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
 
         if (customizeExists) {
           const customizeContent = await fs.readFile(customizePath, 'utf8');
-          const yaml = require('js-yaml');
-          const customizeYaml = yaml.load(customizeContent);
+          const yaml = require('yaml');
+          const customizeYaml = yaml.parse(customizeContent);
 
           // Detect what fields are customized
           if (customizeYaml) {
@@ -2085,18 +2085,21 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
           customizeData = yaml.parse(customizeContent);
         }
 
-        // Build agent answers from customize data
+        // Build agent answers from customize data (filter empty values)
         const answers = {};
         if (customizeData.persona) {
-          Object.assign(answers, customizeData.persona);
+          Object.assign(answers, filterCustomizationData(customizeData.persona));
         }
         if (customizeData.agent?.metadata) {
-          Object.assign(answers, { metadata: customizeData.agent.metadata });
+          const filteredMetadata = filterCustomizationData(customizeData.agent.metadata);
+          if (Object.keys(filteredMetadata).length > 0) {
+            Object.assign(answers, { metadata: filteredMetadata });
+          }
         }
-        if (customizeData.critical_actions) {
+        if (customizeData.critical_actions && customizeData.critical_actions.length > 0) {
           answers.critical_actions = customizeData.critical_actions;
         }
-        if (customizeData.memories) {
+        if (customizeData.memories && customizeData.memories.length > 0) {
           answers.memories = customizeData.memories;
         }
 
@@ -2153,8 +2156,8 @@ If AgentVibes party mode is enabled, immediately trigger TTS with agent's voice:
       let manifest = null;
       if (await fs.pathExists(manifestPath)) {
         const manifestContent = await fs.readFile(manifestPath, 'utf8');
-        const yaml = require('js-yaml');
-        manifest = yaml.load(manifestContent);
+        const yaml = require('yaml');
+        manifest = yaml.parse(manifestContent);
         installedModules = manifest.modules || [];
       }
 
diff --git a/tools/cli/installers/lib/core/manifest-generator.js b/tools/cli/installers/lib/core/manifest-generator.js
index 9532cad7..b25581cf 100644
--- a/tools/cli/installers/lib/core/manifest-generator.js
+++ b/tools/cli/installers/lib/core/manifest-generator.js
@@ -1,6 +1,6 @@
 const path = require('node:path');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const crypto = require('node:crypto');
 const { getSourcePath, getModulePath } = require('../../../lib/project-root');
 
@@ -480,10 +480,9 @@ class ManifestGenerator {
       ides: this.selectedIdes,
     };
 
-    const yamlStr = yaml.dump(manifest, {
+    const yamlStr = yaml.stringify(manifest, {
       indent: 2,
-      lineWidth: -1,
-      noRefs: true,
+      lineWidth: 0,
       sortKeys: false,
     });
 
diff --git a/tools/cli/installers/lib/core/manifest.js b/tools/cli/installers/lib/core/manifest.js
index ce12304f..743b2564 100644
--- a/tools/cli/installers/lib/core/manifest.js
+++ b/tools/cli/installers/lib/core/manifest.js
@@ -11,7 +11,7 @@ class Manifest {
    */
   async create(bmadDir, data, installedFiles = []) {
     const manifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
-    const yaml = require('js-yaml');
+    const yaml = require('yaml');
 
     // Ensure _cfg directory exists
     await fs.ensureDir(path.dirname(manifestPath));
@@ -28,10 +28,9 @@ class Manifest {
     };
 
     // Write YAML manifest
-    const yamlContent = yaml.dump(manifestData, {
+    const yamlContent = yaml.stringify(manifestData, {
       indent: 2,
-      lineWidth: -1,
-      noRefs: true,
+      lineWidth: 0,
       sortKeys: false,
     });
 
@@ -48,12 +47,12 @@ class Manifest {
    */
   async read(bmadDir) {
     const yamlPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
-    const yaml = require('js-yaml');
+    const yaml = require('yaml');
 
     if (await fs.pathExists(yamlPath)) {
       try {
         const content = await fs.readFile(yamlPath, 'utf8');
-        const manifestData = yaml.load(content);
+        const manifestData = yaml.parse(content);
 
         // Flatten the structure for compatibility with existing code
         return {
@@ -79,7 +78,7 @@ class Manifest {
    * @param {Array} installedFiles - Updated list of installed files
    */
   async update(bmadDir, updates, installedFiles = null) {
-    const yaml = require('js-yaml');
+    const yaml = require('yaml');
     const manifest = (await this.read(bmadDir)) || {};
 
     // Merge updates
@@ -101,10 +100,9 @@ class Manifest {
     const manifestPath = path.join(bmadDir, '_cfg', 'manifest.yaml');
     await fs.ensureDir(path.dirname(manifestPath));
 
-    const yamlContent = yaml.dump(manifestData, {
+    const yamlContent = yaml.stringify(manifestData, {
       indent: 2,
-      lineWidth: -1,
-      noRefs: true,
+      lineWidth: 0,
       sortKeys: false,
     });
 
@@ -526,9 +524,9 @@ class Manifest {
 
       try {
         if (await fs.pathExists(configPath)) {
-          const yaml = require('js-yaml');
+          const yaml = require('yaml');
           const content = await fs.readFile(configPath, 'utf8');
-          configs[moduleName] = yaml.load(content);
+          configs[moduleName] = yaml.parse(content);
         }
       } catch (error) {
         console.warn(`Could not load config for module ${moduleName}:`, error.message);
diff --git a/tools/cli/installers/lib/custom/handler.js b/tools/cli/installers/lib/custom/handler.js
index 94dad5e3..6289aa57 100644
--- a/tools/cli/installers/lib/custom/handler.js
+++ b/tools/cli/installers/lib/custom/handler.js
@@ -1,7 +1,7 @@
 const path = require('node:path');
 const fs = require('fs-extra');
 const chalk = require('chalk');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { FileOps } = require('../../../lib/file-ops');
 const { XmlHandler } = require('../../../lib/xml-handler');
 
diff --git a/tools/cli/installers/lib/ide/_base-ide.js b/tools/cli/installers/lib/ide/_base-ide.js
index 0451e73e..f870194c 100644
--- a/tools/cli/installers/lib/ide/_base-ide.js
+++ b/tools/cli/installers/lib/ide/_base-ide.js
@@ -346,7 +346,7 @@ class BaseIdeSetup {
       } else if (entry.isFile() && entry.name === 'workflow.yaml') {
         // Read workflow.yaml to get name and standalone property
         try {
-          const yaml = require('js-yaml');
+          const yaml = require('yaml');
           const content = await fs.readFile(fullPath, 'utf8');
           const workflowData = yaml.parse(content);
 
@@ -454,7 +454,7 @@ class BaseIdeSetup {
               // Check for standalone: true in YAML frontmatter
               const frontmatterMatch = content.match(/^---\s*\n([\s\S]*?)\n---/);
               if (frontmatterMatch) {
-                const yaml = require('js-yaml');
+                const yaml = require('yaml');
                 try {
                   const frontmatter = yaml.parse(frontmatterMatch[1]);
                   standalone = frontmatter.standalone === true;
diff --git a/tools/cli/installers/lib/ide/antigravity.js b/tools/cli/installers/lib/ide/antigravity.js
index e4f024e6..b921b4de 100644
--- a/tools/cli/installers/lib/ide/antigravity.js
+++ b/tools/cli/installers/lib/ide/antigravity.js
@@ -45,7 +45,7 @@ class AntigravitySetup extends BaseIdeSetup {
       const injectionConfigPath = path.join(sourceModulesPath, moduleName, 'sub-modules', 'antigravity', 'injections.yaml');
 
       if (await this.exists(injectionConfigPath)) {
-        const yaml = require('js-yaml');
+        const yaml = require('yaml');
 
         try {
           // Load injection configuration
diff --git a/tools/cli/installers/lib/ide/claude-code.js b/tools/cli/installers/lib/ide/claude-code.js
index 06ff1d86..56131e44 100644
--- a/tools/cli/installers/lib/ide/claude-code.js
+++ b/tools/cli/installers/lib/ide/claude-code.js
@@ -44,7 +44,7 @@ class ClaudeCodeSetup extends BaseIdeSetup {
       const injectionConfigPath = path.join(sourceModulesPath, moduleName, 'sub-modules', 'claude-code', 'injections.yaml');
 
       if (await this.exists(injectionConfigPath)) {
-        const yaml = require('js-yaml');
+        const yaml = require('yaml');
 
         try {
           // Load injection configuration
diff --git a/tools/cli/installers/lib/ide/gemini.js b/tools/cli/installers/lib/ide/gemini.js
index c2e6191e..82746abf 100644
--- a/tools/cli/installers/lib/ide/gemini.js
+++ b/tools/cli/installers/lib/ide/gemini.js
@@ -1,6 +1,6 @@
 const path = require('node:path');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { BaseIdeSetup } = require('./_base-ide');
 const chalk = require('chalk');
 const { AgentCommandGenerator } = require('./shared/agent-command-generator');
diff --git a/tools/cli/installers/lib/ide/kiro-cli.js b/tools/cli/installers/lib/ide/kiro-cli.js
index 1263a803..47f2a29d 100644
--- a/tools/cli/installers/lib/ide/kiro-cli.js
+++ b/tools/cli/installers/lib/ide/kiro-cli.js
@@ -2,7 +2,7 @@ const path = require('node:path');
 const { BaseIdeSetup } = require('./_base-ide');
 const chalk = require('chalk');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 
 /**
  * Kiro CLI setup handler for BMad Method
diff --git a/tools/cli/installers/lib/ide/opencode.js b/tools/cli/installers/lib/ide/opencode.js
index 2296a40a..cf5e8eec 100644
--- a/tools/cli/installers/lib/ide/opencode.js
+++ b/tools/cli/installers/lib/ide/opencode.js
@@ -2,7 +2,7 @@ const path = require('node:path');
 const fs = require('fs-extra');
 const os = require('node:os');
 const chalk = require('chalk');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { BaseIdeSetup } = require('./_base-ide');
 const { WorkflowCommandGenerator } = require('./shared/workflow-command-generator');
 const { TaskToolCommandGenerator } = require('./shared/task-tool-command-generator');
diff --git a/tools/cli/installers/lib/ide/shared/module-injections.js b/tools/cli/installers/lib/ide/shared/module-injections.js
index 9a4448b0..6e38ee10 100644
--- a/tools/cli/installers/lib/ide/shared/module-injections.js
+++ b/tools/cli/installers/lib/ide/shared/module-injections.js
@@ -1,6 +1,6 @@
 const path = require('node:path');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { glob } = require('glob');
 const { getSourcePath } = require('../../../../lib/project-root');
 
diff --git a/tools/cli/installers/lib/modules/manager.js b/tools/cli/installers/lib/modules/manager.js
index a5b790de..73e9b6ab 100644
--- a/tools/cli/installers/lib/modules/manager.js
+++ b/tools/cli/installers/lib/modules/manager.js
@@ -1,9 +1,10 @@
 const path = require('node:path');
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const chalk = require('chalk');
 const { XmlHandler } = require('../../../lib/xml-handler');
 const { getProjectRoot, getSourcePath, getModulePath } = require('../../../lib/project-root');
+const { filterCustomizationData } = require('../../../lib/agent/compiler');
 
 /**
  * Manages the installation, updating, and removal of BMAD modules.
@@ -12,7 +13,7 @@ const { getProjectRoot, getSourcePath, getModulePath } = require('../../../lib/p
  *
  * @class ModuleManager
  * @requires fs-extra
- * @requires js-yaml
+ * @requires yaml
  * @requires chalk
  * @requires XmlHandler
  *
@@ -312,7 +313,7 @@ class ModuleManager {
     // Read module config for metadata
     try {
       const configContent = await fs.readFile(configPath, 'utf8');
-      const config = yaml.load(configContent);
+      const config = yaml.parse(configContent);
 
       // Use the code property as the id if available
       if (config.code) {
@@ -387,7 +388,7 @@ class ModuleManager {
       if (configPath) {
         try {
           const configContent = await fs.readFile(configPath, 'utf8');
-          const config = yaml.load(configContent);
+          const config = yaml.parse(configContent);
           if (config.code === moduleName) {
             return modulePath;
           }
@@ -427,14 +428,14 @@ class ModuleManager {
     if (await fs.pathExists(rootCustomConfigPath)) {
       try {
         const customContent = await fs.readFile(rootCustomConfigPath, 'utf8');
-        customConfig = yaml.load(customContent);
+        customConfig = yaml.parse(customContent);
       } catch (error) {
         console.warn(chalk.yellow(`Warning: Failed to read custom.yaml for ${moduleName}:`, error.message));
       }
     } else if (await fs.pathExists(moduleInstallerCustomPath)) {
       try {
         const customContent = await fs.readFile(moduleInstallerCustomPath, 'utf8');
-        customConfig = yaml.load(customContent);
+        customConfig = yaml.parse(customContent);
       } catch (error) {
         console.warn(chalk.yellow(`Warning: Failed to read custom.yaml for ${moduleName}:`, error.message));
       }
@@ -569,7 +570,7 @@ class ModuleManager {
     if (await fs.pathExists(configPath)) {
       try {
         const configContent = await fs.readFile(configPath, 'utf8');
-        const config = yaml.load(configContent);
+        const config = yaml.parse(configContent);
         Object.assign(moduleInfo, config);
       } catch (error) {
         console.warn(`Failed to read installed module config:`, error.message);
@@ -700,7 +701,7 @@ class ModuleManager {
 
     try {
       // First check if web_bundle exists by parsing
-      const workflowConfig = yaml.load(yamlContent);
+      const workflowConfig = yaml.parse(yamlContent);
 
       if (workflowConfig.web_bundle === undefined) {
         // No web_bundle section, just write (placeholders already replaced above)
@@ -827,20 +828,23 @@ class ModuleManager {
         let answers = {};
         if (await fs.pathExists(customizePath)) {
           const customizeContent = await fs.readFile(customizePath, 'utf8');
-          const customizeData = yaml.load(customizeContent);
+          const customizeData = yaml.parse(customizeContent);
           customizedFields = customizeData.customized_fields || [];
 
-          // Build answers object from customizations
+          // Build answers object from customizations (filter empty values)
           if (customizeData.persona) {
-            Object.assign(answers, customizeData.persona);
+            Object.assign(answers, filterCustomizationData(customizeData.persona));
           }
           if (customizeData.agent?.metadata) {
-            Object.assign(answers, { metadata: customizeData.agent.metadata });
+            const filteredMetadata = filterCustomizationData(customizeData.agent.metadata);
+            if (Object.keys(filteredMetadata).length > 0) {
+              Object.assign(answers, { metadata: filteredMetadata });
+            }
           }
-          if (customizeData.critical_actions) {
+          if (customizeData.critical_actions && customizeData.critical_actions.length > 0) {
             answers.critical_actions = customizeData.critical_actions;
           }
-          if (customizeData.memories) {
+          if (customizeData.memories && customizeData.memories.length > 0) {
             answers.memories = customizeData.memories;
           }
         }
@@ -852,7 +856,7 @@ class ModuleManager {
         if (await fs.pathExists(coreConfigPath)) {
           const yaml = require('yaml');
           const coreConfigContent = await fs.readFile(coreConfigPath, 'utf8');
-          coreConfig = yaml.load(coreConfigContent);
+          coreConfig = yaml.parse(coreConfigContent);
         }
 
         // Check if agent has sidecar
@@ -1017,7 +1021,7 @@ class ModuleManager {
 
     for (const agentFile of yamlFiles) {
       const agentPath = path.join(sourceAgentsPath, agentFile);
-      const agentYaml = yaml.load(await fs.readFile(agentPath, 'utf8'));
+      const agentYaml = yaml.parse(await fs.readFile(agentPath, 'utf8'));
 
       // Check if agent has menu items with workflow-install
       const menuItems = agentYaml?.agent?.menu || [];
diff --git a/tools/cli/lib/agent-analyzer.js b/tools/cli/lib/agent-analyzer.js
index e10ab85b..ae834a09 100644
--- a/tools/cli/lib/agent-analyzer.js
+++ b/tools/cli/lib/agent-analyzer.js
@@ -1,4 +1,4 @@
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const fs = require('fs-extra');
 
 /**
@@ -91,7 +91,7 @@ class AgentAnalyzer {
    */
   async analyzeAgentFile(filePath) {
     const content = await fs.readFile(filePath, 'utf8');
-    const agentYaml = yaml.load(content);
+    const agentYaml = yaml.parse(content);
     return this.analyzeAgentObject(agentYaml);
   }
 
diff --git a/tools/cli/lib/agent/compiler.js b/tools/cli/lib/agent/compiler.js
index 42a66418..71aa326c 100644
--- a/tools/cli/lib/agent/compiler.js
+++ b/tools/cli/lib/agent/compiler.js
@@ -313,7 +313,11 @@ async function compileAgent(yamlContent, answers = {}, agentName = '', targetPat
   // Apply customization merges before template processing
   // Handle metadata overrides (like name)
   if (answers.metadata) {
-    agentYaml.agent.metadata = { ...agentYaml.agent.metadata, ...answers.metadata };
+    // Filter out empty values from metadata
+    const filteredMetadata = filterCustomizationData(answers.metadata);
+    if (Object.keys(filteredMetadata).length > 0) {
+      agentYaml.agent.metadata = { ...agentYaml.agent.metadata, ...filteredMetadata };
+    }
     // Remove from answers so it doesn't get processed as template variables
     const { metadata, ...templateAnswers } = answers;
     answers = templateAnswers;
@@ -353,6 +357,36 @@ async function compileAgent(yamlContent, answers = {}, agentName = '', targetPat
   };
 }
 
+/**
+ * Filter customization data to remove empty/null values
+ * @param {Object} data - Raw customization data
+ * @returns {Object} Filtered customization data
+ */
+function filterCustomizationData(data) {
+  const filtered = {};
+
+  for (const [key, value] of Object.entries(data)) {
+    if (value === null || value === undefined || value === '') {
+      continue; // Skip null/undefined/empty values
+    }
+
+    if (Array.isArray(value)) {
+      if (value.length > 0) {
+        filtered[key] = value;
+      }
+    } else if (typeof value === 'object') {
+      const nested = filterCustomizationData(value);
+      if (Object.keys(nested).length > 0) {
+        filtered[key] = nested;
+      }
+    } else {
+      filtered[key] = value;
+    }
+  }
+
+  return filtered;
+}
+
 /**
  * Process TTS injection markers in content
  * @param {string} content - Content to process
@@ -431,4 +465,5 @@ module.exports = {
   buildPersonaXml,
   buildPromptsXml,
   buildMenuXml,
+  filterCustomizationData,
 };
diff --git a/tools/cli/lib/config.js b/tools/cli/lib/config.js
index 1f7c2ad8..a7825030 100644
--- a/tools/cli/lib/config.js
+++ b/tools/cli/lib/config.js
@@ -1,5 +1,5 @@
 const fs = require('fs-extra');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const path = require('node:path');
 const packageJson = require('../../../package.json');
 
@@ -18,7 +18,7 @@ class Config {
     }
 
     const content = await fs.readFile(configPath, 'utf8');
-    return yaml.load(content);
+    return yaml.parse(content);
   }
 
   /**
diff --git a/tools/cli/lib/platform-codes.js b/tools/cli/lib/platform-codes.js
index d539503a..bdf0e48c 100644
--- a/tools/cli/lib/platform-codes.js
+++ b/tools/cli/lib/platform-codes.js
@@ -1,6 +1,6 @@
 const fs = require('fs-extra');
 const path = require('node:path');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { getProjectRoot } = require('./project-root');
 
 /**
@@ -20,7 +20,7 @@ class PlatformCodes {
     try {
       if (fs.existsSync(this.configPath)) {
         const content = fs.readFileSync(this.configPath, 'utf8');
-        this.config = yaml.load(content);
+        this.config = yaml.parse(content);
       } else {
         console.warn(`Platform codes config not found at ${this.configPath}`);
         this.config = { platforms: {} };
diff --git a/tools/cli/lib/yaml-format.js b/tools/cli/lib/yaml-format.js
index 66dbe3d9..3c38b921 100755
--- a/tools/cli/lib/yaml-format.js
+++ b/tools/cli/lib/yaml-format.js
@@ -1,6 +1,6 @@
 const fs = require('node:fs');
 const path = require('node:path');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const { execSync } = require('node:child_process');
 
 // Dynamic import for ES module
@@ -57,11 +57,10 @@ async function formatYamlContent(content, filename) {
     }
 
     // Parse and re-dump YAML to format it
-    const parsed = yaml.load(fixedContent);
-    const formatted = yaml.dump(parsed, {
+    const parsed = yaml.parse(fixedContent);
+    const formatted = yaml.stringify(parsed, {
       indent: 2,
-      lineWidth: -1, // Disable line wrapping
-      noRefs: true,
+      lineWidth: 0, // Disable line wrapping
       sortKeys: false, // Preserve key order
     });
     // Ensure POSIX-compliant final newline
@@ -96,7 +95,6 @@ async function processMarkdownFile(filePath) {
     const [fullMatch, yamlContent] = match;
     const formatted = await formatYamlContent(yamlContent, filePath);
     if (formatted !== null) {
-      // Remove trailing newline that js-yaml adds
       const trimmedFormatted = formatted.replace(/\n$/, '');
 
       if (trimmedFormatted !== yamlContent) {
diff --git a/tools/cli/lib/yaml-xml-builder.js b/tools/cli/lib/yaml-xml-builder.js
index 6f5db1a5..b8b2de58 100644
--- a/tools/cli/lib/yaml-xml-builder.js
+++ b/tools/cli/lib/yaml-xml-builder.js
@@ -1,4 +1,4 @@
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const fs = require('fs-extra');
 const path = require('node:path');
 const crypto = require('node:crypto');
@@ -64,13 +64,13 @@ class YamlXmlBuilder {
   async loadAndMergeAgent(agentYamlPath, customizeYamlPath = null) {
     // Load base agent
     const agentContent = await fs.readFile(agentYamlPath, 'utf8');
-    const agentYaml = yaml.load(agentContent);
+    const agentYaml = yaml.parse(agentContent);
 
     // Load customization if exists
     let merged = agentYaml;
     if (customizeYamlPath && (await fs.pathExists(customizeYamlPath))) {
       const customizeContent = await fs.readFile(customizeYamlPath, 'utf8');
-      const customizeYaml = yaml.load(customizeContent);
+      const customizeYaml = yaml.parse(customizeContent);
 
       if (customizeYaml) {
         // Special handling: persona fields are merged, but only non-empty values override
diff --git a/tools/validate-agent-schema.js b/tools/validate-agent-schema.js
index 54140139..b351f8ec 100644
--- a/tools/validate-agent-schema.js
+++ b/tools/validate-agent-schema.js
@@ -12,7 +12,7 @@
  */
 
 const { glob } = require('glob');
-const yaml = require('js-yaml');
+const yaml = require('yaml');
 const fs = require('node:fs');
 const path = require('node:path');
 const { validateAgentFile } = require('./schema/agent.js');
@@ -49,7 +49,7 @@ async function main(customProjectRoot) {
 
     try {
       const fileContent = fs.readFileSync(filePath, 'utf8');
-      const agentData = yaml.load(fileContent);
+      const agentData = yaml.parse(fileContent);
 
       // Convert absolute path to relative src/ path for module detection
       const srcRelativePath = relativePath.startsWith('src/') ? relativePath : path.relative(project_root, filePath).replaceAll('\\', '/');