WFCORE-154 - Patching does not process subdirectories

WFLY: https://issues.jboss.org/browse/WFCORE-154
6.x:  https://bugzilla.redhat.com/show_bug.cgi?id=1134735
6.3.x: https://bugzilla.redhat.com/show_bug.cgi?id=1136365


PRs:
WFLY: https://github.com/wildfly/wildfly-core/pull/231
6.x: https://github.com/jbossas/jboss-eap/pull/1790
6.3.x: https://github.com/jbossas/jboss-eap/pull/1789