On Windows I have just converted my application installer from Izpack to JPackage and because of the structure created by JPackage I had to make some code changes to allow my application to find various config files, basically they are copied from app folder to C:\Users\Username\Appdata.... on first start (but bit more complicated than that).
I am now using JPackage on Linux, and the application copies config files from app to $HOME/.appname. However whereas on Windows app is a subfolder relative to launcher with Linux its now in ../lib/app so the code doesnt work
So I have to make some linux specific changes, but it got me wondering am I doing something very wrong here in order for me to have to make these changes ?