Stefan Beller wrote:

> I'll resend it with a warning (using say()).

Thanks, makes sense.

> I think we have 2 bugs and this is merely fixing the second bug.

I'm fearing that there are more than two.

[...]
>   $ git init confused-head
>   $ (cd confused-head && git branch test \
>         $(git commit-tree $(git write-tree) -m test))
>   $ git clone --no-checkout  --depth=1 \
>         --separate-git-dir=test.git confused-head/.git test
> Cloning into 'test'...
> warning: --depth is ignored in local clones; use file:// instead.
> done.
>
>   $ git -C test.git config remote.origin.fetch
>   $ echo $?
> 1
>
> (A) Despite the warning of --depth having no impact, the
>   omission thereof changes the repository state.
> (B) There is no remote.origin.fetch configuration, which
>   is weird. See builtin/clone.c:830, that states for this case:

I can reproduce the issue without submodules and without --local,
as follows:

        git init --bare empty.git
        git init --bare almost-empty.git
        git -C ~/src/git push $(pwd)/almost-empty HEAD:refs/heads/upstream

        git clone --single-branch file://$(pwd)/empty.git
        git clone --single-branch file://$(pwd)/almost-empty.git

        git -C almost-empty.git branch -D upstream

        git -C empty fetch
        git -C almost-empty fetch

Expected result:
Both fetches succeed.

Actual result:
First fetch succeeds, second produces
"fatal: Couldn't find remote ref HEAD".

Note that empty.git and almost-empty.git are basically identical.
The difference instead lies in the clones' .git/config files:

diff --git 1/empty/.git/config 2/almost-empty/.git/config
index b51bb0d..ee21198 100644
--- 1/empty/.git/config
+++ 2/almost-empty/.git/config
@@ -4,7 +4,4 @@
        bare = false
        logallrefupdates = true
 [remote "origin"]
-       url = file:///tmp/t/empty.git
-[branch "master"]
-       remote = origin
-       merge = refs/heads/master
+       url = file:///tmp/t/almost-empty.git

Thanks,
Jonathan

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