Err, I'm sorry, I was sure that I had answered your question by email but I can't find it myself.
There is a one-time migration plan: If session.conf does not exist, then the same keys will be read from geany.conf. That covers users upgrading from 1.38 (or earlier) to 1.39/2.0, so almost all users. There is no plan yet for the time after (I hope to complete the transition before the final realease). There is no plan for git master users.