bug: depth 1 and recursive update of submodules broke in 2.9.0

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When I try to ```git clone --depth 1 --recursive
https://github.com/davidhalter/jedi-vim.git``` in 2.9.0, it fails with
the message: ```
Cloning into 'jedi-vim'...
remote: Counting objects: 37, done.
remote: Compressing objects: 100% (27/27), done.
remote: Total 37 (delta 1), reused 16 (delta 0), pack-reused 0
Unpacking objects: 100% (37/37), done.
Checking connectivity... done.
Submodule 'jedi' (https://github.com/davidhalter/jedi.git) registered
for path 'jedi'
Cloning into '/home/stephanos/jedi-vim/jedi'...
error: no such remote ref 995a6531225ba0b65e1ff863d97e5404d989047b
Fetched in submodule path 'jedi', but it did not contain
995a6531225ba0b65e1ff863d97e5404d989047b. Direct fetching of that
commit failed.
```, while with git 2.8.3 it succeeds. The commit
995a6531225ba0b65e1ff863d97e5404d989047b exists.
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