#1268: Restore handling of visibility

During the refactoring of Descriptors I had implemented visibility as a setting on
the Project Descriptor. Apparently the wiring was never finished or regressed because
the visibility is not taken into account when provided.

With this commit I have restored the functionality to filter on specific visibilities.
#1268: Removed obsolete methods and properties from parser
Merge branch 'develop' into feature/1268
1268: Fix unit test and add feature
Merge branch 'develop' of github.com:phpDocumentor/phpDocumentor2 into feature/1268

Conflicts:
	src/phpDocumentor/Parser/Command/Project/ParseCommand.php
Merge pull request #1275 from mvriel/feature/1268

#1268: Restore handling of visibility