populate: check the hooks and submodules of Git work trees

git submodule update uses the .git of a submodule as it finds it in the
work tree: a repository of its own, with configuration that runs
commands, or a file naming a repository elsewhere.  So git_problems
also requires each .git below the work tree to be a file naming a
repository in .git/modules.  And it refuses hooks in .git/hooks, which
populate's Git doesn't run, but Nix's does, writing the lock file of a
flake in a git source.

git-submodule plants a submodule's .git in the work tree: a repository
of its own whose configuration names a filter, and a file naming a
repository elsewhere.  The fixture withsub has gitsrc as its submodule
sub.

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