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This is technically an invalid configuration, but should fail more gracefully. Create a Linux system type but target MacOS X. This gets you a connection that contains the "Shell Processes" subsystem. Expand one of the filters in the subsystem - get an InvalidThreadStateException. This is thrown explicitly from HostShellProcessAdapter since the underlying shell process is still active.
Changing title to reflect symptom. Create a Linux Host using all the "ssh" services. Create a .bash_logout script as follows: sleep 1 Attempt to connect and get an InvalidThreadStateException. When the "Shell Processes" subsystem starts it gets this when retrieving user names on init. java.lang.IllegalThreadStateException at org.eclipse.rse.services.shells.HostShellProcessAdapter.exitValue(HostShellProcessAdapter.java:85) at org.eclipse.rse.internal.subsystems.processes.shell.linux.LinuxProcessHelper.populateUsernames(LinuxProcessHelper.java:132) at org.eclipse.rse.internal.subsystems.processes.shell.linux.LinuxShellProcessService.initService(LinuxShellProcessService.java:190) at org.eclipse.rse.subsystems.processes.servicesubsystem.ProcessServiceSubSystem.initializeSubSystem(ProcessServiceSubSystem.java:195) at org.eclipse.rse.core.subsystems.AbstractConnectorService.initializeSubSystems(AbstractConnectorService.java:298) at org.eclipse.rse.core.subsystems.AbstractConnectorService.connect(AbstractConnectorService.java:413) at org.eclipse.rse.core.subsystems.SubSystem.connect(SubSystem.java:2255) at org.eclipse.rse.internal.ui.actions.SystemConnectAllSubSystemsAction$ConnectAllJob.run(SystemConnectAllSubSystemsAction.java:69) at org.eclipse.core.internal.jobs.Worker.run(Worker.java:55)
