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I tried this and in fact it does not seem to work?
Building on master in workspace /data/demeter/dev/jenkins-build/jobs/RunAsfTests10/workspace/mainJob/jobs/RunAsfTests10/workspace/RunAsfTests10/jdk=IBM-JDK-7
RTC : checkout...
RTC Checkout : Source control setup
RTC Checkout : Accepting changes into workspace "JenkinsRunAsfTests10" ...
FATAL: RTC : checkout failure: Cannot create sandbox at /data/demeter/dev/jenkins-build/jobs/RunAsfTests10/workspace/mainJob/jobs/RunAsfTests10/workspace/RunAsfTests10/jdk=IBM-JDK-7 because one already exists at /data/demeter/dev/jenkins-build/jobs/RunAsfTests10/workspace/mainJob
com.ibm.team.filesystem.client.FileSystemStatusException: Status ERROR: com.ibm.team.filesystem.client code=0 Cannot create sandbox at /data/demeter/dev/jenkins-build/jobs/RunAsfTests10/workspace/mainJob/jobs/RunAsfTests10/workspace/RunAsfTests10/jdk=IBM-JDK-7 because one already exists at /data/demeter/dev/jenkins-build/jobs/RunAsfTests10/workspace/mainJob null
at com.ibm.team.filesystem.client.internal.copyfileareas.CopyFileAreaManager.createCopyFileArea(CopyFileAreaManager.java:309)
at com.ibm.team.filesystem.client.internal.copyfileareas.CopyFileAreaManager.createCopyFileArea(CopyFileAreaManager.java:1)
at com.ibm.team.filesystem.client.internal.SharingManager.register(SharingManager.java:1002)
at com.ibm.team.build.internal.hjplugin.rtc.RepositoryConnection.checkout(RepositoryConnection.java:363)
at com.ibm.team.build.internal.hjplugin.rtc.RTCFacade.checkout(RTCFacade.java:387)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:60)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37)
at java.lang.reflect.Method.invoke(Method.java:611)
at com.ibm.team.build.internal.hjplugin.RTCFacadeFactory$RTCFacadeWrapper.invoke(RTCFacadeFactory.java:92)
at com.ibm.team.build.internal.hjplugin.RTCCheckoutTask.invoke(RTCCheckoutTask.java:107)
at com.ibm.team.build.internal.hjplugin.RTCCheckoutTask.invoke(RTCCheckoutTask.java:31)
at hudson.FilePath.act(FilePath.java:906)
As you can see the 2 checkout directories are adjacent and not nested but it still complains about the sandbox (maybe because they are both using the same repository workspace)?