[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
[DOC] Normalizing @headerfile file.h to @headerfile <file.h>
[DOC] Improved sorting in the dox templates.
[DOC] Links in Terminal functions and sorting of links.
[DOC] Beefing up documentation of chainSeedsGlobally() somewhat.
[DOC] Small dox fix.
[DOC] Adding type links to startsWith().
[DOC] Extending documentation of splitString().
[DOC] Documentation now automatically shortens unambiguous links.

E.g. JoinStrategiesTags#JournaledCompact is unambiguous, but
String#length is not since there are other #length functions.
Merge pull request #471 from holtgrewe/feature/dox_finalization

Improvement to dox system and documentation
[DOC] Improvements to dox HTML and CSS.
[FIX] Normalizing line endings in master.
Merge branch 'hotfix/master_line_endings' into hotfix/develop_line_endings

Conflicts:
	core/apps/fiona/compute_gain.cpp
[DOC] Fixing typos in API documentation.
Merge pull request #475 from holtgrewe/fix/395

[DOC] Fixing typos in API documentation.
[FIX] Translating both rNextId and rID when reading BAM.

Fixes seqan/seqan issue #421.
Merge pull request #476 from holtgrewe/fix/421

[FIX] Translating both rNextId and rID when reading BAM.