I just commented on the ticket
http://scala-ide-portfolio.assembla.com/spaces/scala-ide/tickets/1000155-its-impossible-to-add-line-numbers-debug-info-to-compiled-project
In short, it works with the latest beta09 (breakpoints can be inserted) but there is an annoying error popup displayed.
Are you using the 2.0.0-beta09? If yes, and this still does not work properly for you, please update the ticket with additional information.
-- Mirco