All I will do is paste the stackoverflow question below. It covers the commands I made in chronological order and the way I would have expected git to behave differently. So I did git pull home_subfolder while in usb_subfolder. Can't remember the immediate output, but it included a part about two repos having no commits in common. Would have been wiser for git to just error out with a message that in one of the folders there is not git repository. At all times git status in home_subfolder gives branch master Working directory clean This is so stupid considering the circumstances. Doing again git pull home_subfolder at all times from usb_folder now returns U in front of 2 files in home_folder and A in front of another file and then says Pull is not possible because you have unmerged files Had the bright idea to do git clone home_subfolder from the usb_subfolder because of my worries going away when git status in home_subfolder conforted me that there must be nothing bad about the situation. Therefore I suspect that now doing git pull usb_subfolder from home_subfolder will do the same broken result as above. I do not want to resolve merge conflicts because git doesn't error out with a sane message of the situation when it should. I just want to get the home_subfolder and usb_subfolder repositories state to where it was before my breakage generating git pull and git clone commands. Ubuntu 14.04 64 bit, git 1.9.1. Thank you for your time.
