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

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') {