Hook fileserver tests into test runner

This should have been done when these tests were first created but I wasn't aware that subdirectories weren't automatically picked up by the test runner. This commit sets the appropriate options for the test runner to be able to run the fileserver tests. 

There have also been some changes to the back-end fileservers inside salt. For the time being, I have disabled the gitfs tests and made some small changes to the ```roots``` integration test to re-align it with current code in develop.