Publish to Wildfly AS does not update files

I think I am on JBIDE product 4.2.0.Final (but features show as 3.6.0.Final and Plugins as 3.0.0.Final-v20141016)

I have an EAR Maven project published to Wildfly 8.x.

there is a file in the project TOPLEVEL/src/main/application/META-INF/jboss-deployment-structure.xml

If this file is edited and saved, and I perform publish operation on server. The change is never made to the deployments directory.

If I manually delete the file from the deployments direcory, then perform clean operation and publish operation and full publish operation, the file is never re-crearted.

The only way is to REMOVE EAR module from server, clean server, stop server, ADD EAR module to server, publish server, start server.

Now the file is updated.

I also note that I have a number of workspace JPA/JAR projects that should be included in the EAR in the lib/* folder but they are never copied there.

I have found a copy in a folder like workspace\.metadata\.plugins\org.jboss.ide.eclipse.as.core\WildFly_8.1.0.Final\tempRemoteDeploy\ in here are the JARs I expected to find in the server runtime folder wildfly-8.1.0.Final\standalone\deployments\com.company.ear\lib**

The timestamps on the files in this directory appear to be up-to-date at each publish event.

As a workaround I use "Make As Deployable" on the file workspace\com.company.ear\target\com.company.ear-1.2.3-SNAPSHOW.ear and I use a manual Maven build profile to create this file.