The clue to "undo" a merge is reflog+reset. It's well explained here:
Use git reflog (which basically shows a log of commits, merges, checkouts,
everything) to find the previous state you want to reset to.
If you get a merge conflict, read the console output from git carefully. You
usually can orient yourself and see what's going on with a "git status".
After you've fixed up the conflicts, you have to git add the files, and then
commit (this will be *the* merge commit).
Your mergetool is basically just for helping with the fixing conflicts
parts, and I think it does a "git add" if the "merge was successful".
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