patch: handle if S points to a subdirectory of a git repo

If PATCHTOOL = "git", SRC_URI fetches from a git repo and S points to
a subdirectory of the checked out sources, then we were erroneously
initialising the subdirectory as its own git repo. Check if the returned
top-level repo directory is a subdirectory of WORKDIR and do not
run initialise the source directory if that is the case.

(This was a regression introduced with OE-Core revision
6184b56a, however we didn't have a test
that verified the behaviour.)

Signed-off-by: Paul Eggleton <paul.eggleton@microsoft.com>
Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>
(cherry picked from commit 9cca53a2)
Signed-off-by: Steve Sakoman <steve@sakoman.com>