~/Synapse/plugins Synapse creates a folder called server-shared. All Plugins which are placed in it will be loaded by all Servers no matter which port they are running on. It is not recommended placing a plugin in both folders because then the plugin will be loaded 2 times.config.syml/permission.syml is placed inside ~/Synapse/configs/server-{port} and if the files exist the Server will use them instead of the ones in server-shared. By Reloading the Server they will not check again where the files are, so it is not recommended changing the locations of these two files while the Server is running~/Synapse/configs/server-{port} and if the files exist the Server will use them instead of the one in server-shared. By Reloading the Server they will not check again where the files are, so it is not recommended changing the locations of these two files while the Server is running