Removed outdated JDT reference

Will use git submodule and update on the next commit
Updated submodule dependencies

wall updated to latest version (some changes to modref that I am
interested in)

(These versions are what i gathered from looking at the plug-ins view in
Eclipse for org.eclipse.jdt.core, org.eclipse.jdt.core.manipulation and
org.eclipse.jdt.ui)

org.eclipse.jdt references tag v20120814-155456
org.eclipse.jdt.ui references tag v20120814-144251