In case others find this thread in the future... This same error happens for 16.2 with tomcat 7.0.x (I'm specifically using 7.0.72). The fixes in issue 27801 to bootstrap.iml and build.xml fixed it.

Note: One can always checkout/update to the latest revision of 16.2 branch and these fixes will be included, but our group always checks out the revision of the branch that we have deployed on our production system so we are developing against the same revision we deploy into (which often isn't the latest of the branch) so I had to add the fixes myself.