Where eclipse keeps plugin preferences

Eclipse keeps the plugin preferences (and templates in the case of  VEditor) in the workspace under

./.metadata/.plugins/org.eclipse.core.runtime/.settings/net.sourceforge.veditor.prefs

Project natures

Project natures are used to customize a generic IProject. The configure() method of IProjectNature can be used to add builders to a project.

IProject resources

Programmers are discouraged from deriving from IProject. Instead if you want to associate an object with IProject, use setSessionProperty. This method is defined in IResource witch IProject derives from. It is also possible to store a string associated with resource by using setPersistentProperty. This property is actually stored on disk and is persistent across sessions.

Also, to get notification of a resource change, use IResourceChangeListener/IResourceChangeEvent.