How do I manage conflicts with git submodules?

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Well, its not technically managing conflicts with submodules (ie: keep this but not that), but I found a way to continue working…and all I had to do was pay attention to my git status output and reset the submodules:

git reset HEAD subby
git commit

That would reset the submodule to the pre-pull commit. Which in this case is exactly what I wanted. And in other cases where I need the changes applied to the submodule, I’ll handle those with the standard submodule workflows (checkout master, pull down the desired tag, etc).

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