Even simpler by cloning into a new folder:

$ git clone https://git.zx2c4.com/cgit .
...
$ git submodule update --init --recursive
Submodule 'git' (https://git.kernel.org/pub/scm/git/git.git)
registered for path 'git'
Cloning into '/git-cgit/git'...
Submodule path 'git': checked out '69986e19ffcfb9af674ae5180689ab7bbf92ed28'
Submodule 'sha1collisiondetection'
(https://github.com/cr-marcstevens/sha1collisiondetection.git)
registered for path 'git/sha1collisiondetection'
Cloning into '/git-cgit/git/sha1collisiondetection'...
Submodule path 'git/sha1collisiondetection': checked out
'855827c583bc30645ba427885caa40c5b81764d2'

$ git apply --verbose --check ../0005-git2.29.1.patch
Checking patch Makefile...
Checking patch git...

$ git apply --verbose ../0005-git2.29.1.patch
Checking patch Makefile...
Checking patch git...
warning: unable to rmdir 'git': Directory not empty
Applied patch Makefile cleanly.
Applied patch git cleanly.

$ make
...
$ make test
...
    SUBDIR tests
ok 1 - extract Git version from Makefile
not ok 2 - test Git version matches Makefile
#
# ( cat ../../git/GIT-VERSION-FILE || echo "No GIT-VERSION-FILE" ) |
# sed -e "s/GIT_VERSION[ ]*=[ ]*//" -e "s/\\.dirty$//" >git_version &&
# sed -e "s/-/./g" makefile_version >makefile_git_version &&
# test_cmp git_version makefile_git_version
#
not ok 3 - test submodule version matches Makefile
#
...
The patch is attached (copied from first post)
-- 
Jean-Christophe