How do you fix a bad merge, and replay your good commits onto a fixed merge?

Question

I accidentally committed an unwanted file (filename.orig while resolving a merge) to my repository several commits ago, without me noticing it until now. I want

Answer 1

The simplest way I found was suggested by leontalbot (as a comment), which is a post published by Anoopjohn. I think its worth its own space as an answer:

(I converted it to a bash script)

#!/bin/bash
if [[ $1 == "" ]]; then
    echo "Usage: $0 FILE_OR_DIR [remote]";
    echo "FILE_OR_DIR: the file or directory you want to remove from history"
    echo "if 'remote' argument is set, it will also push to remote repository."
    exit;
fi
FOLDERNAME_OR_FILENAME=$1;

#The important part starts here: ------------------------

git filter-branch -f --index-filter "git rm -rf --cached --ignore-unmatch $FOLDERNAME_OR_FILENAME" -- --all
rm -rf .git/refs/original/
git reflog expire --expire=now --all
git gc --prune=now
git gc --aggressive --prune=now

if [[ $2 == "remote" ]]; then
    git push --all --force
fi
echo "Done."

All credits goes to Annopjohn, and to leontalbot for pointing it out.

NOTE

Be aware that the script doesn't include validations, so be sure you don't make mistakes and that you have a backup in case something goes wrong. It worked for me, but it may not work in your situation. USE IT WITH CAUTION (follow the link if you want to know what is going on).