[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.

Jira: https://issues.jboss.org/browse/WFLY-3305