I split out the Apps directory from my main repository. It's now a git submodule, but it's purely optional because Apps just has my domain-specific files. The supported domains like UPWELLING are still in the main code.
While I was at it, I split out Old_Apps as it's own repo, containing files for domains I'm going to stop maintaining. That too could be loaded as a submodule if you so choose. Some of those domains are Paul Budgell's and he has moved on to using other models.