What if we wanted to drop sha1collisiondetection/ as a submodule and replace it with a copy of what's now in sha1dc/? I ran into this with another project, but here's a way to reproduce it on git.git:
( rm -rf /tmp/git && git clone g...@github.com:git/git.git /tmp/git cd /tmp/git && git tag nuke-before && git submodule update --init && git rm -r .gitmodules sha1collisiondetection && git commit -m"Nuke sha1dc submodule" && cp -Rvp sha1dc sha1collisiondetection && git add sha1collisiondetection && git commit -m"Now it's not a submodule" && git tag nuke-after && git reset --hard nuke-before && git submodule update --init && # skip this and the below won't fail git reset --hard nuke-after && # Emulate someone doing a pull git ls-tree HEAD | grep sha1collisiondetection && # OK, shows "tree" not "commit" test $(git rev-parse HEAD) == $(git -C sha1collisiondetection/ log -1 --pretty=format:%H) && echo OK || echo WTF ) This results in a really bizarre state where according to ls-tree sha1collisiondetection is a tree at the current commit: 040000 tree 81583289d96bdde4b366c243ab524ea28d895ea5 sha1collisiondetection But git still believes there's a submodule there for some reason, and shows the log for the upstream sha1collisiondetection project: git -C sha1collisiondetection/ log -1 commit 19d97bf (HEAD, origin/master, origin/HEAD, master) Merge: 3f14d1b c93f0b4 Author: Dan Shumow <shu...@gmail.com> Date: Sat Jul 1 12:36:15 2017 -0700 Merge pull request #37 from avar/fixup-pull-request-34 Fix endian detection logic for Sparc, little endian BSD etc. Doing: git submodule deinit sha1collisiondetection Does nothing to help, then I thought it might be: git config -f .git/config -l|grep ^submodule submodule.sha1collisiondetection.active=true submodule.sha1collisiondetection.url=https://github.com/cr-marcstevens/sha1collisiondetection.git But running: git config --remove-section submodule.sha1collisiondetection Doesn't help either, neither does removing the index: rm .git/index && git reset --hard If you then do: rm -rf .git/modules You'll get this error: git -C sha1collisiondetection/ log -1 fatal: Not a git repository: /tmp/git/sha1collisiondetection/../.git/modules/sha1collisiondetection But I can't see what's still referencing it. This problem is avoided if, as noted with a comment I skip: git submodule update --init But I shouldn't need to remember to de-init a submodule before moving to a new commit that doesn't have it, least I end up in some seemingly unrecoverable state. Am I missing something obvious here?