Eclipse workspace & active sets
I prefer to have one workspace and put all my projects into this one work space instead of making multiple workspaces to organize projects. I then use active sets to organize the clutter in the Project Explorer. This way I set up the workspace preferences once. Typically all my projects are Dynamic Web Projects so setting up one Server to me is more efficient than having to do this for multiple workspaces.
But What I found is that unless you also close the project before moving it out of the active set, the Problems view still shows entries for projects not in the active set. Is there a configuration setting to modify this behavior?
EDIT: OK I just learned about Windows Working Sets from this link http://blog.empiregpservices.com/post.cfm/eclipse-window-working-sets. You can change, edit or create new working sets from one interface and all your views will obey this choice. And as nanda points out below you can Configure Contents of the Problems View using the down arrow view menu. Then choose the scope to be Windows working set Voila! All views can now be in sync!
You can configure the Problem view only to show error from the active sets. See the toolbar on the upper right of the view.