FWIW, I tried the following quick change based on the info. provided
by Junio and it seems to "fix" my original problem. I'll let you
experts figure out if we need a more complete fix or not.

diff --git a/submodule.c b/submodule.c
index 5a62aa2..23443a7 100644
--- a/submodule.c
+++ b/submodule.c
@@ -960,6 +960,9 @@ unsigned is_submodule_modified(const char *path,
int ignore_untracked)
                return 0;

+       /* stuff submodule git dir into env var */
+       set_git_dir(git_dir);

        if (ignore_untracked)
@@ -1279,5 +1282,9 @@ void prepare_submodule_repo_env(struct argv_array *out)
        for (var = local_repo_env; *var; var++) {
                if (strcmp(*var, CONFIG_DATA_ENVIRONMENT))
                        argv_array_push(out, *var);
+               if (strcmp(*var, GIT_DIR_ENVIRONMENT))
+                       argv_array_pushf(out, "%s=%s", GIT_DIR_ENVIRONMENT,
+                                        get_git_dir());


On Wed, Aug 31, 2016 at 9:42 AM, Junio C Hamano <gits...@pobox.com> wrote:
> Uma Srinivasan <usriniva...@twitter.com> writes:
>>> I might suggest to update prepare_submodule_repo_env() so that the
>>> spawned process will *NOT* have to guess where the working tree and
>>> repository by exporting GIT_DIR (set to "git_dir" we discover above)
>>> and GIT_WORK_TREE (set to "." as cp.dir is set to the path to the
>>> working tree of the submodule).  That would stop the "git status" to
>>> guess (and fooled by a corrupted dir/.git that is not a git
>>> repository).
>> Here's where I am struggling with my lack of knowledge of git
>> internals and the implementation particularly in the context of how
>> environment variables are passed from the parent to the child process.
> Ah, I was primarily addressing Jacob in the latter part of my
> message, as he's looked at similar things in his recent topic.
>> Are you suggesting that we set up the child process environment array
>> (the "out" argument) in prepare_submodule_repo_env() to include
>> CONFIG_DATA_ENVIRONMENT that is there now?
> I was wondering if we should unconditionally stuff GIT_DIR=<the
> repository location for the submodule> in the cp.env_array passed to
> the function prepare_submodule_repo_env().  As cp.dir will be set to
> the submodule's working tree, there is no need to set GIT_WORK_TREE
> and export it, I think, although it would not hurt.
> After all, we _are_ going into a separate and different project's
> repository (that is what a submodule is), and we _know_ where its
> repository data (i.e. GIT_DIR) and the location of its working tree
> (i.e. GIT_WORK_TREE).  There is no reason for the process that will
> work in the submodule to go through the usual "do we have .git in
> our $cwd that is a repository?  if not how about the parent directory
> of $cwd?  go up until we find one and that directory is the top of
> the working tree" discovery.
> More importantly, this matters when your GIT_DIR for the submodule
> is somehow corrupt.  The discovery process would say "there is .git
> in $cwd but that is not a repository" and continue upwards, which
> likely would find the repository for the top-level superproject,
> which definitely is _not_ want you want to happen.  And one way to
> avoid it is to tell the setup.c code that it should not do the
> discovery by being explicit.

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