Also, I'm not sure that ever deleting an .isdeploying marker is ever appropriate.

when removing a module from AS runtime marker files are not removed automatically --------------------------------------------------------------------------------- Key: JBIDE-18862 URL: https://issues.jboss.org/browse/JBIDE-18862 Project: Tools (JBoss Tools) Issue Type: Feature Request Components: server Environment: Windiws7 64bit, JDK 8u25 Reporter: Darryl Miles Priority: Minor Fix For: 4.2.2.Final, 4.3.0.Alpha1 module removal does not delete the various marker files relating to it: *.undeployed *.dodeploy The same should be true when ADDING a module, it should clean out any marker files. Setup an deploy-inhibiting marker file to ensure it won't try to deploy it before the *.ear is full written. Write out the*.ear file. Then adjust the marker files as necessary to reflect the intended state of the module (if it should be started then remove the inhibiting marker file in the previous step).