diff --git a/app/nginx_deploy_gui.py b/app/nginx_deploy_gui.py
index e38f199..ae09775 100644
--- a/app/nginx_deploy_gui.py
+++ b/app/nginx_deploy_gui.py
@@ -6,61 +6,11 @@ from PySide6.QtWidgets import (
 )
 from PySide6.QtCore import Qt
 from datetime import datetime
+from logic.deployment_controller import DeploymentController
+from logic.logger import Logger
 
 LOG_FILE = "logs/nginx_deploy_gui.log"
 
-class Logger:
-    def __init__(self, log_widget):
-        self.log_widget = log_widget
-        self.log_file = open(LOG_FILE, "a")
-
-    def log(self, message):
-        timestamp = datetime.now().strftime("[%Y-%m-%d %H:%M:%S]")
-        full_message = f"{timestamp} {message}\n"
-        self.log_widget.append(full_message)
-        self.log_file.write(full_message)
-        self.log_file.flush()
-
-    def close(self):
-        self.log_file.close()
-
-class DeploymentController:
-    def __init__(self, logger):
-        self.logger = logger
-        # These will be set by the UI
-        self.ssh_key = None
-        self.config_dir = None
-
-    def preflight_checks(self):
-        self.logger.log("Running pre-flight checks...")
-        # Stub: implement actual checks
-        self.logger.log("Pre-flight checks complete.")
-
-    def scan_domains(self):
-        self.logger.log("Scanning for domains in configs...")
-        # Stub: implement domain scan
-        self.logger.log("Domain scan complete.")
-
-    def transfer_files(self):
-        self.logger.log("Transferring files to remote server...")
-        # Stub: implement file transfer
-        self.logger.log("File transfer complete.")
-
-    def remote_ops(self):
-        self.logger.log("Performing remote file operations...")
-        # Stub: implement remote ops
-        self.logger.log("Remote operations complete.")
-
-    def run_certbot(self):
-        self.logger.log("Prompting user for Certbot run...")
-        # Stub: implement certbot prompt and run
-        self.logger.log("Certbot step complete.")
-
-    def cleanup(self):
-        self.logger.log("Performing cleanup...")
-        # Stub: implement cleanup
-        self.logger.log("Cleanup complete.")
-
 class MainWindow(QMainWindow):
     def __init__(self):
         super().__init__()
@@ -148,7 +98,15 @@ class MainWindow(QMainWindow):
         self.controller.remote_ops()
 
     def run_certbot(self):
-        self.controller.run_certbot()
+        # Prompt user for Certbot confirmation
+        from PySide6.QtWidgets import QMessageBox
+        reply = QMessageBox.question(self, 'Run Certbot',
+            'Run Certbot for the discovered domains?',
+            QMessageBox.Yes | QMessageBox.No, QMessageBox.No)
+        if reply == QMessageBox.Yes:
+            self.controller.run_certbot(lambda prompt: True)
+        else:
+            self.controller.run_certbot(lambda prompt: False)
 
     def cleanup(self):
         self.controller.cleanup()