Fixes #1017: Erroneous behaviour of --hidden

The hidden command line option should allow phpDocumentor
to traverse hidden folders when added but phpDocumentor
functioned the other way around; only when the hidden option
was provided it did not descend into hidden directories.

To clear up any confusion will phpDocumentor now not descend
into hidden directories and is the text altered to make this
more clear.
Merge branch 'develop' into feature/1017

Conflicts:
	src/phpDocumentor/Parser/Command/Project/ParseCommand.php
Merge pull request #1262 from mvriel/feature/1017

Fixes #1017: Erroneous behaviour of --hidden