I’m using 4.0.1 and I notice that if I make edits to a User Library (remove a JAR, add a JAR, etc), the changes are not deployed. I must re-deploy the app to realize the changes.
Right now, automatically detecting and redeploying due to user library changes is not supported. It’s simply something that doesn’t come up much so we’ve never added ‘auto recognition’ for it since it would almost surely break a running application due to library locking issues with running servers. As you’ve discovered, the workaround is to manually ask MyEclipse to redeploy your project that was affected by the change.