Hi Fred,
I have tried to remove
<directory>src/main/webapp</directory>
as you suggested above,
but when selecting jbas7 profile, WTP starts to copy contents of
src/main/webapp-jee6
to
web-resources/WEB-INF/src
so web.xml is misplaced in WEB-INF/src/WEB-INF/web.xml.
This seems as very strange consequence, so I have tried several times with same result.