EXECUTE: import decent sized project, i.e. GWT project from central and follo the readme regarding tooling
EXECUTE: after Run As have been done, right click server and press Clean...
ASSERT: clean is done and publish goes on and then in the end .dodeploy file occurrs

What actually seem to happen is deploymen is removed, dir added, then .dodeploy and then file copying occurs - causing the scanner to pickup partially deployed project.