Fix Paths Discovery / Added extensive test for index_prefix

# The larasearch:paths command could not handle directories with directories inside of it.  This fixes that.
# The larasearch:paths command would get tripped up when the world 'class' appeared at the end of a comment.
# Added extensive testing for index_prefix to ensure the prefix would not be applied twice.  I initially thought it would be better to mock out responses from accessors but found a better way to test in the end though left the getters and setters in place.
# phpunit/phpunit 4.5.*@dev does not point to dev-master anymore so had to update to 4.6.*@dev.