Set the CWD before applying a git patch

Summary:
If in a subdirectory, any changes made in a different location
is missed from the patch with no errors from git. The other
option was to run some logic to compare the files being changed.

Test Plan:
Run arc patch from a subdirectory that would miss some files
previously.

Reviewers: epriestley

Reviewed By: epriestley

CC: Korvin, aran

Maniphest Tasks: T3733

Differential Revision: https://secure.phabricator.com/D7167