If you change the server file and exit the program, it looks like it's saving that change to spigotgui.settings, but when you re-open the program it's reset to server.jar
I looked at your code, I think it's because you're saving the actual File object in the Settings object rather than the path of the file. I don't think input.readObject is going to just automatically deserialize the way you seem to expect it to.
I think if you save the path as a separate string and just.... initialize the File based on the string you'll probably be fine.
If you change the server file and exit the program, it looks like it's saving that change to spigotgui.settings, but when you re-open the program it's reset to server.jar
I looked at your code, I think it's because you're saving the actual File object in the Settings object rather than the path of the file. I don't think input.readObject is going to just automatically deserialize the way you seem to expect it to.
I think if you save the path as a separate string and just.... initialize the File based on the string you'll probably be fine.