"submodule" mistake and a problem

Hi,

I did this and now am confused/stuck...

- I have an existing (long standing) project in git with an upstream in github
- I added a subdirectory which I had forgotten was itself a git
project (i.e. it has its own .git directory)
- I committed the subdirectory (git add /path/to/subdir;  git commit -m ....)
- I pushed the latest version upstream

....at this point I realised that only the directory name had been pushed. SO...

- git rm /path/to/subdir resulted in fatal: pathspec
'/path/to/subdir/' did not match any files
- so I deleted it manually, re-copied the directory and removed its
.git directory

...I now cannot add or commit the directory. Git just ignores it. I
have grepped and searched and kind find no reference to this directory
anywhere. I am completely stumped.

Can anybody help? I don't want this to be a git subdirectory, I just
want to be able to add the files (without the .git directory)

Cheers :)