Fix Missing VagrantFile-clean
startup shouldn't move file, it should copy it
Changed the xdebug to enable dev environment and clean to use prod environment
Added recomended php extensions
Removed mcrypt due to broken package
Revert "Changed the xdebug to enable dev environment and clean to use prod environment"

This reverts commit 1f58d2d05daa70806db52c75a9166ca1afff7c5e.
Clean option shouldn't have dev environment enabled