Same thing when downgrading a package by "apt-get install" e.g. after
you remove a PPA. I think apt could try to retain auto/manual states in
these cases. But could there be a case where dependencies change when
you upgrade/downgrade? Would it be safer to search the packages that
depend on the automatically installed packages and tell apt to downgrade
it and the dependencies? I doubt current apt can downgrade dependencies
automatically.

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https://bugs.launchpad.net/bugs/1482959

Title:
  Upgrading/downgrading a package with "apt-get install" should not make
  the package marked as manually installed, if it was not before

Status in apt package in Ubuntu:
  New

Bug description:
  I'm using Ubuntu 15.10 dev with apt 1.0.9.10ubuntu6 and if a specific
  package gets upgraded with "apt-get install" it gets also set to
  manual installed if it is an automatic installed package but this
  could be unexpected for the user. Maybe similar if the user tries to
  install an already up-to-date automatic installed package apt could
  tell the user then that the package got set to manual installed.

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