Merge pull request #410 from holtgrewe/hotfix/fiona_allowindels

[FIX] Enabling indel mode in fiona again.
[FIX] Normalizing line endings by default in app tests.

This caused problems with nightly builds.
Merge pull request #419 from holtgrewe/hotfix/app_tests_normalize_crlf

[HOTFIX] Normalizing line endings by default in app tests (develop).