Revert "Use virtual file based resource manager to make sure deployment overlays work correctly with Undertow"

This reverts commit bd7fa6ed03188a74c89663826d7e6b77df64d8df.

This caused problems JSP, as getResource() on a jar would return the mounted directory, rather than the jar file.
WFLY-2598: fixes scheduledTimerFutures synchronization between timer creation and execution
[WFLY-2595] Rewrite the logging DUP's. Ensure the undeploy unregisters the log contexts so class loaders and log contexts aren't leaked.
WFLY-2398 fix InflowJarTestCase test fail on full profile
RESTEASY-991 Add integration test that JAX-RS components are CDI beans
with appropriate scope
https://issues.jboss.org/browse/WFLY-1063 Provide CLI preferences (support for variables)
[WFLY-671] re-enabled test, corrected assertion msg, reduced timezones
add Principal to subject

Principal is only added to subject if we use RemotingConnectionCredential or when there is no Principal at all.
If we have valid principal we forget about it.

This causes org.jboss.security.auth.spi.RoleMappingLoginModule to be broken.
I'm not sure if this fix is correct (we can always get Principal from callbackHandler in LoginModule).

Another question what to do with roles? (JbossCallbackHandler don't contain this information) and what to do with roles added in LoginModule
WFLY-2618 : Intermittent 'AssertionError: expected:<200> but was:<500>' in org.jboss.as.test.manualmode.ws.ReloadWSDLPublisherTestCase.testHelloStringAfterReload
The test was failing intermittently because per default the JVM is using HttpConnection with keep-alive and a timeout of 5s.
By setting the keep-alive to false in the setup and setting it to the value before the test on tear down we ensure a more stable test.
Merge pull request #5562 from stuartwdouglas/undertow

Revert "Use virtual file based resource manager to make sure deployment ...
Merge pull request #5563 from emmartins/WFLY-2598

WFLY-2598: fixes scheduledTimerFutures synchronization between timer cre...
Merge commit 'refs/pull/5564/head' of github.com:wildfly/wildfly

Conflicts:
	testsuite/integration/smoke/src/test/java/org/jboss/as/test/smoke/deployment/rar/tests/inflow/InflowTestCase.java
Merge pull request #5565 from mkouba/RESTEASY-991

RESTEASY-991 Add integration test that JAX-RS components are CDI beans
Merge pull request #5566 from aloubyansky/cli-variables

https://issues.jboss.org/browse/WFLY-1063 Provide CLI preferences (cli variables)
Merge pull request #5567 from jamezp/WFLY-2595

[WFLY-2595] Rewrite the logging DUP's. Ensure the undeploy unregisters the log contexts so class loaders and log contexts aren't leaked.
Merge pull request #5569 from adietish/WFLY-753

[WFLY-671] re-enabled test, corrected assertion msg, reduced timezones
Merge pull request #5576 from ehsavoie/WFLY-2618

WFLY-2618 : Intermittent 'AssertionError: expected:<200> but was:<500>' ...
[WFLY-2616] Add SEVERE logging level to the valid list of levels.
Revert "Merge commit 'refs/pull/5460/head' of github.com:wildfly/wildfly"

This reverts commit eab955383f9f0647f00e5782998de88600ec62a1, reversing
changes made to 3259a05a2ef9601f3515c5a1cc89f1a9cbd419a3.
Merge pull request #5570 from wojtask9/patch-1

add Principal to subject