I think many of the duplicates assigned to this bug are actually a separate bug.
One bug is about "packages installed by the updater are not released when new 
versions installed with the image". 
The other is "storage view should aggregate different versions of packages with 
the same name".

So, I'm splitting this bug in two, and proposing a branch for the
second.

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https://bugs.launchpad.net/bugs/1479001

Title:
  Older version of a user installed click is not updated by custom or
  base pre-installed clicks with a more recent version

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