lib/oe/patch: fix PATCHTOOL = "git" with source in a subdirectory

lib/oe/patch: fix PATCHTOOL = "git" with source in a subdirectory

For recipes that have their actual source in a subdirectory of what is
fetched (e.g. mkelfimage), we need to find the root of the repository
within the GitApplyTree code that attempts to set up the required git
hooks and use that, rather than expecting the root to be the same as
${S}.

Signed-off-by: Paul Eggleton <paul.eggleton@linux.intel.com>
Signed-off-by: Richard Purdie <richard.purdie@linuxfoundation.org>