> I assume that what gets deployed uses the pom to build the app, is that true?
The toolset itself does not necessarily use pom.xml at all. If you have m2e installed only, then it will not use pom.xml at all. It uses a file in {your.project}/.settings/org.eclipse.wst.common.component which is an xml file driving the server deployment model. It maps folders that should be included in the deployment among other things.
m2e-wtp is another add-on which I assume you are using. This file tries to make the component.xml file match the behaviour of pom.xml as closely as possible.