Currently I store all rules files on the file system (there are lots of versions of them) and load the different versions of them into memory at startup. I would like to change
Once you get into the business of storing multiple version of rules in a data store you are really looking for the Business Rule Management (BRMS) features of Guvnor (in Drools 5.x) or the Drools-WB/KIE-WB workbenches in Drools 6.0.
Those solutions have solved for versioning, storage, and deployment of multiple rule versions out of the box. In short, they will be more robust than a homegrown solution.