Confusing behavior with ignored submodules and `git commit -a`

Hi,

In the past few months have noticed some confusing behavior with ignored submodules. I finally got around to bisecting this to commit 5556808690ea245708fb80383be5c1afee2fb3eb (add, reset: ensure submodules can be added or reset).

Here is a demonstration of the problem:

First some repository initialization with a submodule marked as ignored.

$ git init inner && git -C inner commit --allow-empty -m 'inner 1'
Initialized empty Git repository in /tmp/inner/.git/
[master (root-commit) ef55bed] inner 1
$ git init outer && cd outer
Initialized empty Git repository in /tmp/outer/.git/
$ git submodule add ../inner
Cloning into '/tmp/outer/inner'...
done.
$ echo 1 > foo.txt && git add foo.txt
$ git commit -m 'outer 1'
[master (root-commit) efeb85c] outer 1
 3 files changed, 5 insertions(+)
 create mode 100644 .gitmodules
 create mode 100644 foo.txt
 create mode 160000 inner
$ git config submodule.inner.ignore all
$ git -C inner commit --allow-empty -m 'inner 2'
[master 7b7f0fa] inner 2
$ git status
On branch master
nothing to commit, working tree clean
$

Up to here is all expected. However, if I go to update `foo.txt` and commit with `git commit -a`, changes to inner get recorded unexpectedly. What's worse is the shortstat output of `git commit -a`, and the diff output of `git show` give no indication that the submodule was changed.

$ echo 2 > foo.txt
$ git status
On branch master
Changes not staged for commit:
  (use "git add <file>..." to update what will be committed)
  (use "git checkout -- <file>..." to discard changes in working directory)

        modified:   foo.txt

no changes added to commit (use "git add" and/or "git commit -a")
$ git commit -a -m 'update foo.txt'
[master 6ec564c] update foo.txt
 1 file changed, 1 insertion(+), 1 deletion(-)
$ git show
commit 6ec564c15ddae099c71f01750b4c434557525653 (HEAD -> master)
Author: Michael Forney <mforney@mforney.org>
Date:   Fri Mar 16 20:18:37 2018 -0700

    update foo.txt