question regarding "Clear output directory on rebuild"

Hi,
I have the following Web project structure:

src
web (this is the web root directory)
WEB-INF
classes
all other web root directories

My question:
I have set the output path to "...web\WEB-INF\classes" and switched on the "Clear output directory on rebuild" option, but upon rebuild it opens a popup saying that "... source files exist in the following output path "...\web", and that "Compilation will proceed without clearing the output directory".

Help...