I have a big repository and I sometimes want to remove projects from my
workspace just to keep it clean. However, when I remove a project from the
workspace it is also removed from the repository. The only thing that I can
do is to drop the repository and clone it again from upstream.
I remove the project with unchecked "Delete projects contents from disk"
I just tested this, it seems fine. if I delete a project from the workspace in the usual way (right-click the project root, select 'Delete' from the menu) and don't check the box labelled "Delete project contents on disk (cannot be undone)", I get exactly the desired behavior - the project is no longer in my workspace but the repository is unaffected.
OS X 10.7.4
Eclipse Indigo SR2