The clue to "undo" a merge is reflog+reset. It's well explained here:

<http://stackoverflow.com/questions/2389361/git-undo-a-merge>

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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