Always call zigbee shepherd permit join (in both true and false).

lib/controller.js

@@ -59,9 +59,10 @@ class Controller {
                         logger.warn('`permit_join` set to  `true` in configuration.yaml.');
                         logger.warn('Allowing new devices to join.');
                         logger.warn('Set `permit_join` to `false` once you joined all devices.');
-                        this.zigbee.permitJoin(true);
                     }
 
+                    this.zigbee.permitJoin(settings.get().permit_join);
+
                     // Start timers.
                     this.pollTimer(true);
                     this.softResetTimeout(true);

lib/util/settings.js

@@ -6,6 +6,7 @@ const objectAssignDeep = require(`object-assign-deep`);
 const path = require('path');
 
 const defaults = {
+    permit_join: false,
     advanced: {
         log_directory: path.join(data.getPath(), 'log', '%TIMESTAMP%'),
         log_level: process.env.DEBUG ? 'debug' : 'info',