Ok, I've got a problem that I have no idea how to go about solving.
First, a bit of history:
I pulled from my upstream to bring in changes and merged them with the branch I was working in. At the time, I may have been using a console window with root access. I say this because I noticed a day later I couldn't save to a lot of the files in my local repo. I noticed the owner / group had been changed to root and permissions were 644. After going through and hunting down all of the screwed up files, I then pushed some changes I had made back to my remote working branch.
A week later (now), and I've added several other commits to an open pull request from my remote branch. In the middle of them was the commit I made after fixing my local repo file permissions. I noticed it has some 1200 "empty" files (no changes). I'm a little concerned that merging this pull request upstream could cause big problems and I have no idea how to remove this one commit or if it's even possible...
I tried creating a new branch and using cherry-pick to get all but the one commit, but I've removed files and couldn't merge the older commits that saw a "conflict" between the file that existed at the time and one that no longer exists in the local repo...
Anyway, any thoughts?