tests: submodule: do not rely on config iteration order

The test submodule::lookup::duplicated_path, which tries to verify that
we detect submodules with duplicated paths, currently relies on the
gitmodules file of "submod2_target". While this file has two gitmodules
with the same path, one of these gitmodules has an empty name and thus
does not pass `git_submodule_name_is_valid`. Because of this, the test
is in fact dependent on the iteration order in which we process the
submodules. In fact the "valid" submodule comes first, the "invalid"
submodule will cause the desired error. In fact the "invalid" submodule
comes first, it will be skipped due to its name being invalid, and we
will not see the desired error. While this works on the master branch
just right due to the refactoring of our config code, where iteration
order is now deterministic, this breaks on all older maintenance
branches.

Fix the issue by simply using `cl_git_rewritefile` to rewrite the
gitmodules file. This greatly simplifies the test and also makes the
intentions of it much clearer.

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