OS Linux Mint 19.1
Starting the server through the GUI in '/Home/user/Spigot_1.13.2/' folder, it creates all the files in the '/Home/user' directory creating a file and folder mess .It is creating the 'spigotgui.settings' in the '/Home/user' folder and not in the root directory of the 'Spigot_1.13.2' folder .
Expected behaviour is to create all files and folders in the directory that the server.jar file is in .
If this is Bug please fix and update the Manual with example start script for the GUI if needed
Tested in Windows 10 and directories and files are created in the directory of the sever.jar