Was working on updating a WordPress installation from 3.4.1 to 4.0 while also pulling it out of a multisite install. I have been using Git to keep track of changes along the way (thankfully!). I ran into an upgrade issue and used the following commands to get me back to where I needed to be:

git reset --hard hash

git clean -qfdx

Sources: Revert To A Previous Git Commit, Git Reset Hard Leaves Untracked Files Behind