Fixes

https://github.com/uliska/frescobaldi/commit/199ecf1bdf354d6d05ba4cb5387ed9dcccbcf416 fixes the issue with the `guile-module` warning:
The offending lines had been inserted as a stub for a future development: They are necessary to be able to inject `-e` command line options. But this has turned out to be unnecessary.

When the custom file is included before the other modes it is possible to define all configuration variables there