Eclipse Juno with m2eclipse builds ear but omits war - eclipse

I'm trying to build an application no one has touched in quite a while. It uses Spring and is an ear. The build environment is Eclipse Juno with Maven. When I build the app, an ear file is created but there is no war or other web resources in it. No web-inf folder.
if I go to the project -> properties -> Deployment Assembly there are mappings for source to deploy path, for example:
/src/main/java WEB-INF/classes
/src/main/resources WEB-INF/classes
/src/main/webapp /
/src/test/java WEB-INF/classes
/src/test/resources WEB-INF/classes
The packaging type in the pom is set to ear.
What else do I need to check?

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How to make M2E (Maven for eclipse) include required eclipse projects in WAR

I'm starting to use Maven (M2E) on Eclipse.
I have two projects
->Tools
->Main
The Main project requires the Tools project. I add "Tools" under the "Main"->"Deployment assembly" option, and when exporting to WAR, the WAR will automatically contain also Tools.jar. This is correct.
Now I installed M2E on the Main Project, to manage some spring dependencies. When I edit the pom.xml, Maven starts, and correctly downloads the Spring jars, but it removes the Tools project from the "Deployment assembly" option (it disappear from the org.eclipse.wst.common.component eclipse configuration file)
As a result, when I export the WAR from Eclipse->Export, the war will not contain Tools.jar, so the webapp will not work.
How do I configure pom.xml to do what Eclipse does with the "deployment assembly"?
That is, package all classes and resources and jar dependencies of the Tools project?
I think that I'm missing some understanding of Maven, but I've not been able to google about it?
thank you

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myapp.ear
...META-INF
......application.xml
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I am deploying my app on jboss EAP run time environment and maven is not used in my project.
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Dynamic Web project in Eclipse Neon not including jars from Ear APP-INF/lib

I have a set of projects I am working on in eclipse. An ear with a number of jars in APP_INF/lib and several projects for the wars under the ear. They are all Dynamic web projects. In Kepler and Mars the jars in APP-INF/lib show up as a library in the war projects.
Now I am moving to Neon. I have pulled in the ear and one of the wars and the classes in the war won't compile because the jars from APP-INF/lib are not in the classpath of the war.
Did something change? Is there a settings change I need to make?
I even created a new dynamic web project. I added it the the ear as part of creation. But it too does not contain a library from the ear.
I am running the web app on JBOSS EAP 6.4
Neon.2 Release (4.6.2) Build id: 20161208-0600
I am not sure why it wasn't automatically included, but in the build path, I needed to add the Ear library.

maven and eclipse builds differently the same project

I have a java ear maven project.
When I publish the ear to jboss7 via eclipse it generates an ear and deploys it to jboss.
But when I manually run a maven build of the same project I get a different ear in size and also the name is different.
When eclise builds the project when executing "publish to server", doesnt it use the same build as maven?
I use eclipse juno and maven3. I'm new to maven.
Eclipse uses the .classpath to package the ear that gets deployed to jboss. When you do a manual maven build it is using the pom.xml file to package the ear. If those aren't in sync you could get differences in your ears.