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?
Existing documentation:
https://www.whonix.org/wiki/Whonix_Configuration_Files
The config folder sourceing code for whonix-gw-firewall be viewed here:
https://github.com/Whonix/whonix-gw-firewall/blob/master/usr/bin/whonix_firewall#L27
https://github.com/Whonix/whonix-gw-firewall/blob/5ebca43416269a5fd42c98a80af1b0b3d38adecf/usr/bin/whonix_firewall#L27
Others for whonixcheck etc. look similar.