[FIX] Fixing file extensions in compute_gain's arg parser.
[TEST] App tests for fiona.
Merge pull request #468 from holtgrewe/hotfix/dox_nosetests

[FIX] Fixing dox tests to run with Python nosetests.
Merge pull request #463 from holtgrewe/hotfix/fiona_tests

Changes to fiona and app tests
[FIX] Normalizing line endings in master.
Merge branch 'hotfix/master_line_endings' into hotfix/develop_line_endings

Conflicts:
	core/apps/fiona/compute_gain.cpp
Merge branch 'hotfix/develop_line_endings' of github.com:holtgrewe/seqan into develop

Conflicts:
	core/demos/seeds/seeds_chaining.cpp