[WFLY-3349] Synchronization of cosmetic schema changes with EAP.

The purpose of this commit is to make it easier to verify that the EAP and WildFly schemas are actually in synch.
[WFLY-3305] : :deploy after :undeploy is broken
Fixing issue by updating the marker files for the scanner using the runtime status from the ScannerContext.
Logging a message in case the deployment managed by the scanner was updated through another management tool.
Don't touch the undeployed flag if the deployment is persistent.
Fix issue with persistent flag not being changed during replacement.
Enabling deployment when replacing from the scanner.
Merge pull request #6220 from ehsavoie/WFLY-3305

[WFLY-3305] : :deploy after :undeploy is broken
Merge pull request #6267 from darranl/WFLY-3349

[WFLY-3349] Synchronization of cosmetic schema changes with EAP.