How do I add files in Git to the path of a former submodule?

I have a project that used to contain a submodule, at path mysubmodule. I installed the latest Git from source (1.8.3-rc2) and ran git submodule deinit mysubmodule. I then deleted the .gitmodules file and committed the change. I also deleted the .git directory from the mysubmodule folder.

I'd like to commit the files from mysubmodule into my repo directly now, but git says there are no changes. If I type git add mysubmodule it does nothing. If I type git add mysubmodule/file.txt it says fatal: Path 'mysubmodule/file.txt' is in submodule 'mysubmodule'

I've also discovered if you check out a fresh version of the repo, it creates a mysubmodule directory, despite having no .gitmodules file. And running git submodule init gives you a No submodule mapping found in .gitmodules for path 'mysubmodule' error.

How do I fix this?

Git still think mysubmodule is a submodule, because it is recorded in the index with a special mode "160000".
See "git submodule update needed only initially?" for more.
To check that, as in in this answer, you can do a:

 $ git ls-tree HEAD mysubmodule 
 160000 commit c0f065504bb0e8cfa2b107e975bb9dc5a34b0398  mysubmodule 

That doesn't depend on the presence of the .gitmodule file, or on the content of mysubmodule.

You need to remove that entry from the index first:

 git rm --cached mysubmodule

Then you can proceed.