(Supplied) project files override user settings

[tkemmer]

Project files include a copy of the BALLView INI file, which will be restored when loading, overriding all existing user settings present in the (potentially stale) copy.

In addition to causing problems with different versions of BALLView, this is particularly annoying when using PresentaBALL, as most clicks result in a supplied project file being loaded, rendering the settings menu ludicrous. Another direct implication of using PresentaBALL is not being able to download PDB structures, as the project files ship with an outdated link to the database.

Updating the project files would be a starting point, but it would also only treat the symptoms.