Yeah, that's something I'm trying to think about with the current project that I'm working on. Part of why I brought up mongodb support. Maybe something like datomic would be better.
Starting with simple files is actually really convenient and takes very little effort. Only fixing things that need fixing is a good way to make progress quickly, but it is a little disconcerting not to have many options to switch to.
Maybe building a simple arc-based database would be a good idea, but that also distracts from solving the actual problems I'm working on. Which did not initially include making a new database, as much fun as that would be.
I was working on a simple git-based data storage system for arc as part of my 'metagame' project. Not exactly designed for multi-server use though.