I have downloaded WF 12 and 13, then imported each into Eclipse (Oxygen.3a Release (4.7.3a)), OS is Win 7/x64; then used add-user to set up admin user. Then from both the command line and from within Eclipse, when the software starts up all of the xml configuration files get deployed at the same time despite the fact that the --server-config=standalone.xml parameter is present in either environment. What's worse, it starts versioning them and re-deploying them over and over and over again.

15:45:42,229 INFO [org.jboss.as.clustering.infinispan] (ServerService Thread Pool – 66) WFLYCLINF0002: Started client-mappings cache from ejb container
15:45:42,319 INFO [org.jboss.as.server] (ServerService Thread Pool – 39) WFLYSRV0010: Deployed "standalone.xml" (runtime-name : "standalone.xml")
15:45:42,320 INFO [org.jboss.as.server] (ServerService Thread Pool – 39) WFLYSRV0010: Deployed "standalone-load-balancer.xml" (runtime-name : "standalone-load-balancer.xml")
15:45:42,324 INFO [org.jboss.as.server] (ServerService Thread Pool – 39) WFLYSRV0010: Deployed "standalone-ha.xml" (runtime-name : "standalone-ha.xml")
15:45:42,324 INFO [org.jboss.as.server] (ServerService Thread Pool – 39) WFLYSRV0010: Deployed "standalone-full.xml" (runtime-name : "standalone-full.xml")
15:45:42,325 INFO [org.jboss.as.server] (ServerService Thread Pool – 39) WFLYSRV0010: Deployed "standalone-full-ha.xml" (runtime-name : "standalone-full-ha.xml")
15:45:42,326 INFO [org.jboss.as.server] (ServerService Thread Pool – 39) WFLYSRV0010: Deployed "standalone-ee8.xml" (runtime-name : "standalone-ee8.xml")
15:45:42,407 INFO [org.jboss.as.server] (Controller Boot Thread) WFLYSRV0212: Resuming server
15:45:42,410 INFO [org.jboss.as] (Controller Boot Thread) WFLYSRV0060: Http management interface listening on http://127.0.0.1:9990/management
15:45:42,411 INFO [org.jboss.as] (Controller Boot Thread) WFLYSRV0051: Admin console listening on http://127.0.0.1:9990
15:45:42,411 INFO [org.jboss.as] (Controller Boot Thread) WFLYSRV0025: WildFly Full 13.0.0.Final (WildFly Core 5.0.0.Final) started in 6285ms - Started 549 of 746 services (326 se
rvices are lazy, passive or on-demand)
15:45:42,575 INFO [org.jboss.as.server.deployment] (MSC service thread 1-3) WFLYSRV0027: Starting deployment of "standalone.last.xml" (runtime-name: "standalone.last.xml")
15:45:42,578 INFO [org.jboss.as.server.deployment] (MSC service thread 1-1) WFLYSRV0027: Starting deployment of "standalone.boot.xml" (runtime-name: "standalone.boot.xml")
15:45:42,581 INFO [org.jboss.as.server.deployment] (MSC service thread 1-6) WFLYSRV0027: Starting deployment of "standalone.initial.xml" (runtime-name: "standalone.initial.xml")
15:45:42,724 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0010: Deployed "standalone.last.xml" (runtime-name : "standalone.last.xml")
15:45:42,725 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0010: Deployed "standalone.initial.xml" (runtime-name : "standalone.initial.xml")
15:45:42,726 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0010: Deployed "standalone.boot.xml" (runtime-name : "standalone.boot.xml")
15:45:47,921 INFO [org.jboss.as.server.deployment] (MSC service thread 1-3) WFLYSRV0028: Stopped deployment standalone.xml (runtime-name: standalone.xml) in 28ms
15:45:47,928 INFO [org.jboss.as.server.deployment] (MSC service thread 1-8) WFLYSRV0027: Starting deployment of "standalone.xml" (runtime-name: "standalone.xml")
15:45:47,930 INFO [org.jboss.as.server.deployment] (MSC service thread 1-2) WFLYSRV0027: Starting deployment of "standalone.v1.xml" (runtime-name: "standalone.v1.xml")
15:45:47,982 INFO [org.jboss.as.server.deployment] (MSC service thread 1-6) WFLYSRV0028: Stopped deployment standalone.last.xml (runtime-name: standalone.last.xml) in 55ms
15:45:47,984 INFO [org.jboss.as.server.deployment] (MSC service thread 1-3) WFLYSRV0027: Starting deployment of "standalone.last.xml" (runtime-name: "standalone.last.xml")
15:45:48,059 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0016: Replaced deployment "standalone.last.xml" with deployment "standalone.last.xml"
15:45:48,060 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0010: Deployed "standalone.v1.xml" (runtime-name : "standalone.v1.xml")
15:45:48,060 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0016: Replaced deployment "standalone.xml" with deployment "standalone.xml"
15:45:53,233 INFO [org.jboss.as.server.deployment] (MSC service thread 1-3) WFLYSRV0028: Stopped deployment standalone.xml (runtime-name: standalone.xml) in 13ms
15:45:53,236 INFO [org.jboss.as.server.deployment] (MSC service thread 1-6) WFLYSRV0027: Starting deployment of "standalone.v2.xml" (runtime-name: "standalone.v2.xml")
15:45:53,237 INFO [org.jboss.as.server.deployment] (MSC service thread 1-3) WFLYSRV0027: Starting deployment of "standalone.xml" (runtime-name: "standalone.xml")
15:45:53,249 INFO [org.jboss.as.server.deployment] (MSC service thread 1-5) WFLYSRV0028: Stopped deployment standalone.last.xml (runtime-name: standalone.last.xml) in 15ms
15:45:53,252 INFO [org.jboss.as.server.deployment] (MSC service thread 1-7) WFLYSRV0027: Starting deployment of "standalone.last.xml" (runtime-name: "standalone.last.xml")
15:45:53,340 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0016: Replaced deployment "standalone.last.xml" with deployment "standalone.last.xml"
15:45:53,341 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0010: Deployed "standalone.v2.xml" (runtime-name : "standalone.v2.xml")
15:45:53,342 INFO [org.jboss.as.server] (DeploymentScanner-threads - 1) WFLYSRV0016: Replaced deployment "standalone.xml" with deployment "standalone.xml"