So, m2e and m2e-wtp are different. I've never been quite clear on that.
If you change your pom.xml you get an error that says the project is out of configuration or something like that and running Maven -> Update Project Configuration... updates that file? If you have changed your dependencies and don't update that file, not only will the list of libraries entitled Maven Dependencies be out of date, but the project itself won't incorporate the correct libraries into the lib when you deploy it. Is that right? And I assume any structural changes to that app you have made in the pom like <includes> and <excludes> won't make it into the deployed app unless you run Update Project Configuration... as well.
The bottom line is that running Maven -> Update Project Configuration... synchronizes the org.eclipse.wst.common.component to the pom.xml. True?
That takes some of the magic out of it ( that is a good thing)
Thanks.
TDR