sources vs. Java packages roots

projects gurus,

is it design or (known?) bug that there is no relationship between 
sources and Java packages roots?

Namely when I add directory containing sources and mark some of subdirs 
as Java packages roots these are not removed from project when I remove 
this sources diretory. It means that Add + Remove doesn't return my 
project to previous state. Also it is not clear to me why predefined 
java package root is not contained in some sources (maybe it is better 
not to clutter the UI with an additional sources folder).

Looks unnatural to me so please keep this mail as some kind of usability 
feedback.

Radim