Allow users to configure modules using multiple source roots including Test source roots and have Illuminated Cloud deploy to Force.com from these source roots and reconcile back into the appropriate source roots on retrieve.
Also allow arbitrary sub-foldering for metadata, in particular the classes, triggers, pages, and components folders. On deployment add a comment denoting the "package", e.g.:
and on retrieval use that comment to place retrieved metadata in the correct sub-folder if specified.
Also for static resources, sub-folders could be used for automatic archive creation on deploy and archive expansion on retrieve.