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Installing customizations using AMPs into a new Alfresco repository is pretty easy, there isn’t much room for configuration overwriting other configuration.  In older systems that have been installed by a client or in systems that have multiple SI’s customizations installed it maybe the case, especially in Share, where configuration from one amp overwrites the configuration of another amp.  You can get into difficult to detect problems depending on the order in which amps are applied to Alfresco (probably alphanumeric, last one wins).