I've observed that the windows version is saving user generated files, like gpx routes, in a subfolder of the EV4 program folder. This on the contrary of the Windows philosophy (as far as I am aware), which is to save user specific files not in the program folder, which is also protected (which might cause difficulties when attempting to delete such files again). Instead, such files should be saved in a subfolder of the users Documents folder. Any chance you can change this and keep the program folder free of any user interaction required?
This is a long standing wish for myself too. I won't bother you about details, but this is/was an inheritence of our multiplatform development system. To be honest I forgot all about this, but I will look into this further to see if we can finally make this change now.
