Created FileHelperImpl

Changed FileHelper interface to not be static
Fixed Issues 5, 7, 9

File helper no longer uses static methods, has directory functionality.
Update FileHelperImpl to match new interface
Change ArrayList to Collection in FileHelper

Also removed getTree
Merge pull request #10 from RITHonorsTechCommittee/grdaneault

Grdaneault merging
Merge branch 'master' into jmi4099
Updated getPermission method in UserHelper.java