Prepare for taking MF configurations from DB

Includes:
-Tools to create .db files for standard configurations 
-Fix for one numerical stability problem with geometries imported to DB. The problem did not affect existing configurations (with geometry coming from xml), and the fix was regression-tested.

This fix is needed to be able to finally switch to reading MF geometry and configuration from DB, which will happen in a future (pre)release once a GT with all required payloads becomes available.