[FIX] Normalizing line endings by default in app tests.

This caused problems with nightly builds.
Merge pull request #418 from holtgrewe/hotfix/app_tests_normalize_crlf

[HOTFIX] Normalizing line endings by default in app tests. (master)
[FIX] Normalizing line endings when comparing text files.
Merge pull request #422 from holtgrewe/hotfix/compare_text_file_line_endings

[FIX] Normalizing line endings when comparing text files (master).
[Fix] Converted double align scores to int scores to avoid different 32bit 64bit behaviour.
Merge pull request #428 from skrakau/master

Bisar: converted alignment scores to integers