The submodule merge code is being transitioned away from
add_submodule_odb() to repo_submodule_init(), and the latter does not
support submodules that have their .git directories in the worktree
(instead of in .git/modules). Migrate the test code by calling
absorbgitdirs wherever necessary to place the .git directories of
submodules in .git/modules of the superproject.
Upon further work, there seems to be quite a lot of test code to
migrate, and it might be easier instead to add support for unabsorbed
submodules to repo_submodule_init() (say, following what
open_submodule() in submodule.c does). Feel free to comment on this or
other aspects of the patch set, and in the meantime, I'll investigate
that.