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I have two repos that claim to be clean. One was originally cloned from the other and is used for dev work.

There are a few files that I can see are not the same. However when I try pulling either way it says everything is up to date.

How is this possible?

Did that file miss a commit somehow? ...but shouldn't the difference be noticed regardless?

Do I need a refresh of some sort?

A: 

Maybe you have some commits in repo A branch b, while repo B has no modifications yet in branch b (but may have some modifications in other branches) Meaning a git pull B will return "Already up-to-date."

That or those files with differences are actually ignored (have been removed from the index and are selected by the .gitignore file)

VonC
the files in question are not in my .gitignorehowever on a related note now I'm wondering how to update my index with regard to what should be ignored.
doublejosh
@doublejosh: "on a related note now I'm wondering how to update my index with regard to what should be ignored": see http://stackoverflow.com/questions/2897753/git-status-shows-a-file-that-i-have-listed-explicitly-in-my-gitignore-file/2897782#2897782
VonC
Thanks for the link! On this issue, no branches (as I understand them, explicitly created branches.)
doublejosh
Yeah, double checked (since I haven't done branching yet) there is only a master in each.
doublejosh
A: 

To answer my own question, I've decided to deal with this very odd situation by cloning the original repo and just archiving away the seemingly broken repo.

I assume the problem came from pulling bi-directionally. However it shouldn't have because the change was committed and pulled across.

Perhaps the gnomes were at work on this one. But I still have faith in GIT.

doublejosh