In ProjectViewer it is possible to exclude a folder or a file from the project using right click.
I think that if I reimport ProjectViewer should remember what files are excluded
I like that idea. Basically, a second-pass through the file list will be necessary for it to work with any file import filter.
Now it is possible to combine "directories to ignore" with other import filters on a global or a per-project basis, so the "remove from project" action when you remove a folder from a project should have a checkbox option to add that folder to the "directories to ignore list" so it doesn't get added again later.