TFS configuration cannot see changes of a modified project
If you establish a site (pulled local copy from Azure in my case) and then configure the site to use TFS, it works as expected. If you then delete the local copy, and re-download the same site again, TFS is completely broken. Cannot check files in. "No files to check-in" is all you get. This is permanent and show stopping. Uninstall of WebMatrix and deleting every possible trace of the site in AppData, My Docs, etc, will NOT fix this problem.
There is a bug with managing workspaces – we are looking into it.
One work around here is to fire up VS, go to the 'source control explorer', and delete the auto-created workspace.