Adding a getPatches method that retrieves all of the patch files from the make file
Begin adding code to copy over the patches

#issue #2025459 by theunraveler: Removing sprintf and escapeshellarg transforms since drush_shell_exec will handle them accordingly

Issue #2025459 by theunraveler: Misc failures when makefile, source, or destination directories have spaces or special characters

Fixing setMessage method call. Adding a check to make sure there are no stashs before starting. Adding stash clear after we apply and clean up. Adding some better help text and removing extrenous documentation code

Replacing "git st" with "git status". Adding check environment checks. Adding check to make sure destination is indeed a git repo. Adding check to make sure that patches applied cleanly.