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rake update:all runs git pull on default branches for repositories. Default branches are the branches defined in the Docfile.yml. They are always protected. Direct committing into protected branches are strictly forbidden. And there is a reason for it. When you add a commit to your default branch, you cannot push it, BUT that commit will become a part of your new branch.

When git shows you that there is something wrong after rake update:all, it means that content in your default branch has been changed. You never commit changes to a default branch!

Reset the corresponding default branches in devdocs and subrepositories where you directly added those commit.

git fetch
git checkout master
git reset --hard origin/master

If you work in subrepositories (any local-only branches, stashes):

cd <directory of a subrepo from Docfile>
git fetch
git checkout <branch from Docfile>
git reset --hard origin/<branch from Docfile>

If you never work with subrepositories:

rake multirepo:reinit

CAUTION: multirepo:reinit will remove all the directories and associated git repositories listed in Docfile.