t1600: fix racy index.skipHash test

t1600: fix racy index.skipHash test

The test 1600.6 can fail under --stress due to mtime collisions. Most of
the tests include a removal of the index file to guarantee that the
index is updated. However, the submodule test addded in ee1f0c242ef
(read-cache: add index.skipHash config option, 2023-01-06) did not
include this removal. Thus, on rare occasions, the test can fail because
the index still has a non-null trailing hash, as detected by the helper
added in da9acde14ed (test-lib-functions: add helper for trailing hash,
2023-01-06).

By removing the submodule's index before the 'git -C sub add a' command,
we guarantee that the index is rewritten with the new index.skipHash
config option.

Signed-off-by: Derrick Stolee <derrickstolee@github.com>
Signed-off-by: Junio C Hamano <gitster@pobox.com>