Along these same lines, I have added a RemoveFile to ProjectFactories. And, have also implement Absolute or Relative file handling in the OgreProject factory (part of the DotScene plugin), and allowed the user to change it via the PropertyWindow. Of course, this is not yet saved, but Project saving is next on the agenda as file saving has been completed.
Also, just a note about plugin developers. You do not have to implement a ProjectFactory, for must basic editing of certain files, you would want to implement the IFileFactory, so that a project (from any plugin) could be able to open your file.
If your plugin does not implement neither a Project or FileFactory, you can look at the SceneViewer for an example of how to open up windows, and interact. Once your tool window is being used, you could listen to the PropertyManager changin events, plus, i plan to add an event to OgrePane, so that you know when something else has changed the Ogre scene. Of course, you are free to create your own floating window (or new tab window) that has an OgreWindow that you create + your own scenemanager, so that no one else could mess with your editor's scene/material editing/etc.