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Close application before installing locally-published update

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http://serverfault.com – I'm using Local Update Publisher to publish several software packages to users' machines through WSUS, and it works pretty well for the most part. I have noticed a peculiar issue with Java, though, if an update starts while a Java application is running. The first thing the Java installer does is uninstall the old version of itself, which somehow succeeds, but then it fails to move on and actually install the new version because it finds a Java program running. This leaves the machine without Java, so the next round of update checks finds that Java is not needed. Is there a way I can instruct (HowTos)