The long term solution should be that a package records its origin in
the extended_states file. As a short term solution we can just disable
the plugin as the auto-removable plugin will take care of most of the
important cases. Its currently impossible for the code to distinguish
between a package was was availalbe in the repo at some point and is no
more (i.e. a package that is no longer downloadable) from a package that
got manually installed.

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https://bugs.launchpad.net/bugs/458872

Title:
  Don't mark for removal manually installed packages

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