git subtree pull says that the working tree has modifications, but git status says it doesn't. What gives?

I just had the same problem.From GIT source, error is thrown when command git diff-index HEAD returns result, even if git status says working tree is clean.

To avoid this error, in my case, I re-checkout the current branch of working tree , and everything seems OK : git checkout <branch>

It's a bit confused, but if someone can explain why ...

git reset --hard fixed it to me

From git reset --help

--hard Resets the index and working tree. Any changes to tracked files in the working tree since are discarded.

I got around this now. My problem seemed to me that the repository was brand new: I had never committed anything to it. Once I committed a file to the repo, I was able to move past this error.

However, using the command git subtree add C:\gitTest\repos\subA -d --prefix subA I got the new error:

fatal just how do you expect me to merge 0 trees?

After messing around for a minute, I figured out it requires that a specific revision be passed to it. So this command seems to have succeeded:

git subtree add C:\gitTest\repos\subA HEAD -d --prefix subA

And obviously you don't need the -d debug flag.