It would be nice to have a separate simfactory directory for all user customisations rather than mixing them in with the code. This way, one can update simfactory (or delete/recheckout) without having to extract all changes.
Here is one possible solution:
Allow the user to specify a "sf-config" directory (maybe there is a better name) in the defs.local.ini. Any configuration files, for example mdb entries, scriptfiles etc, should be searched for under sf-config first before looking in the standard location. One could then set
sf-config = simfactory.user
and put local machine definitions and scriptfiles and modifications to the standard ones which are never going to be committed. One could keep the same directory structure under simfactory.user as is in simfactory, or it might be better to just search for files in that directory, since all the files should have different names, and an extra hierarchy is just annoying.