In project's properties, go to Deployment Assembly. Add there the buildpath entries as well which you've manually added as user libraries. It'll end up in
/WEB-INF/lib of the deployed WAR.
You'll need to copy the jar files to the WEB-INF/lib folder: that is where they are supposed to be.
Eclipse should offer you the option of generating a WAR file that includes all the dependencies: I haven't used Web Tools for a good while but one way or another all dependencies have to be in WEB-INF/lib or the class loader won't be able to find them.
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