Files that end with ~ are ignored (backup files by many editors). Files that end with .dpkg-* are ignored (file names used by dpkg conflict resolution). So you could rename these files for example to .dpkg-nouse.
Do we want to rename all the config files to include a .conf extension and then only source those? Any opinions?
The config folder sourceing code for whonix-gw-firewall be viewed here:
Others for whonixcheck etc. look similar.