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@xxxxxxxxxxx> Date: Fri Mar 16 20:18:37 2018 -0700 update foo.txt diff --git a/foo.txt b/foo.txt index d00491f..0cfbf08 100644 --- a/foo.txt +++ b/foo.txt @@ -1 +1 @@ -1 +2 $ There have been a couple occasions where I accidentally pushed local changes to ignored submodules because of this. Since they don't show up in the log output, it is difficult to figure out what actually has gone wrong. Anyway, since the bisected commit (555680869) only mentions add and reset, I'm assuming that this is a regression and not a deliberate behavior change. The documentation for submodule.<name>.ignore states that the setting should only affect `git status` and the diff family. In terms of my expectations, I would go further and say it should only affect `git status` and diffs against the working tree. I took a brief look through the relevant sources, and it wasn't clear to me how to fix this without accidentally changing the behavior of other subcommands. Any help with this issue is appreciated!