From Eclipse Newsgroup:
The warning about the source property
is new with Tomcat 6.0.16 and may be
ignored. WTP adds a "source" attribute
to identify which project in the
workspace is associated with the
context. The fact that the Context
object in Tomcat has no corresponding
source property doesn't cause any
problems.
I realize that this doesn't answer how to get rid of the warning, but I hope it helps.