There is now technology in place to support exclusion filters in the workspace.
You can create an exclusion filter in I20060110 by creating a linked resource
to the "null" file system. The linked resource will hide any file system
resource with the same name, thus acting as an exclusion mechanism.
Maybe it is now a good time to reconsider the investment in Komodo
Update: Thanks for Robert for pointing this one out and I stopped pounding my head (a lot less at least):
apparently you can right click on the directory, select "Properties", and check the "Derived" check box, which will do the trick.