Some of the tests in https://github.com/jbosstools/jbosstools-integration-tests/tree/master/tests/org.jboss.ide.eclipse.as.ui.bot.test will need to be updated to accommodate a slight change in EAP 6.1.

When you deploy a project the log used to contain:
Registering web context: /jsp-project
But now in EAP 6.1.0.DR3 it says:
Register web context: /jsp-project

See the test failure here:
https://jenkins.mw.lab.eng.bos.redhat.com/hudson/view/EAP6/view/EAP6-JBDS/job/eap-60-jbds-compatibility-jbosstools-4.0/lastCompletedBuild/testReport/org.jboss.ide.eclipse.as.ui.bot.test.eap6/DeployJSPProjectEAP6Server/Default___deployProject/

The expected string is actually defined in org.jboss.ide.eclipse.as.ui.bot.test/src/org/jboss/ide/eclipse/as/ui/bot/test/eap6/DeployJSPProjectEAP6Server.java

and the fix would be trivial. But it's probably better to create a new template for 6.1 and have it separate from 6.0.