If you ever created an update that uses MSI rules you are bound to see a warning message letting you know that the scan agent cannot detect an MSI if it was installed per-user and that you should use different rules to help detect if the update is applicable
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In both System Center Updates Publisher (SCUP) and Custom Updates Publishing Tool (CUPT) there are three different types (or sections) of detection rules in the Create/Modify Update Wizard. These rules types are prerequisite, applicability and installed
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