Thanks for your bugreport.

I prepared a new apt upload that will explicitly exclude all direct
dependencies from meta-packages from being marked as automatic installs.
This should fix a lot of the confusion seen here.

In addition to this I have attached a fixup script that will mark the
current direct dependencies of installed meta-packages as manual
installed. It will make a copy of your old state file in
/var/lib/apt/extended_states.fixup-save so if anything goes wrong, you
can still copy it back.

The script requires the latest python-apt to work.

Please test it and let me know if that fixes the issues at hand.

Thanks,
 Michael

** Attachment added: "python-apt script to fix incorrect set auto-installed 
information"
   http://librarian.launchpad.net/6804623/fixup.py

** Changed in: apt (Ubuntu)
       Status: Confirmed => In Progress

-- 
apt wants to autoremove packages i explicitly installed
https://launchpad.net/bugs/86921

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