cmake: Fix PATCH_COMMAND for pigweed

The default version of `patch` available on macOS (2.0-12u11-Apple) does
not fully support `git --diff` format, and fails to create new files
defined in a patch file.

We already depend on `git` to fetch pigweed's sources, so replace
`patch` with `git apply` to improve portability and fix the issue
mentioned above.

Additionally, make the whole PATCH_COMMAND more robust and safe for
re-running by bringing the git tree to a known (clean) state.

Signed-off-by: Filip Jagodzinski <filip.jagodzinski@arm.com>