mounted WTP project, add JSF, seam facet, deploy to tomcat starts failing

I have a WTP project with this structure

project
---input
------javasrc - our *.java files
------libinclude - jar files we want in WEB-INF/lib when done(ie. Web App Libraries)
------libexclude - jar files we don't want in WEB-INF/lib
------webroot - xhtml files
---------WEB-INF - descriptor files

We download jboss tools and then we go into the project properties and click on Facets and add JSF and Seam. This incorrectly adds jars to webroot/WEB-INF/lib directory!!!! Worse yet, now when we deploy to tomcat, it is failing with ClassNotFoundExceptions where if we check out the project with WTP, everything works fine and we can use the server view to deploy to tomcat.

the number one issue is that WTP seems to allow people to manage the jars themselves and JBoss tools is forcing jars to be put in webroot/WEB-INF/lib which is actually incorrect since the jars are in libinclude and that is what is deployed to tomcat when I right click and choose debug on the tomcat server.