Every night, I have SuperDuper! create an image of my hard drive to an external drive. This works great, and has saved me from system failures a number of times.
However, OS X is constantly treating it as if the installation of OS X on that external drive is a part of my actual system rather than just a backup on an external drive. To wit, when I do a Spotlight search all results are duplicated. (Even though I have expressly forbidden Spotlight's indexing of the
/Volumes folder through System Preferences.) Every app in the Mac App Store, when updated, will update the copy on my system and then report again a second time that this app needs to be updated again, and running the update will update this external drive. Apps that request the location of my iPhoto library always list two.
How can I get OS X to just treat that drive like an external drive full of data, rather than as a part of the current OS X installation?