"It seems that this bug can be easily fixed now" - if you know of an
easy fix, do enlighten us, please, preferably in the form of a patch?
As far as I know my comment 14 still stands, and there is no
straightforward way to fix this bug right now.

We have lived with this bug for some time, across two previous LTS
releases (apt only gained the auto-mark changes in Ubuntu 6.10, but
before that the installer used aptitude to install tasks and that had a
similar feature).  It is unfortunate, and it is a bug, and we will fix
it if somebody comes up with a way to do so cleanly while getting the
semantics correct, but it isn't critical (much less "megacritical" -
please don't dilute the value of words by exaggerating!) and it's not
worth attempting to hack a fix in when we're not certain that it has the
right semantics.  Leaving all packages as manually installed is
unsightly but the consequences of this bug are generally limited to not
managing to be clever enough to remove packages that aren't needed any
more.  A flaw in the reverse direction would be much worse, because it
could cause packages to be removed when they are still needed.  Given
that there does not seem to be a clearly correct fix available, it's
better to air on the side of caution.

So, please stop leaving comments about how the priority of this bug
should be increased; it should not.  That does not mean it is not a bug,
and it does not mean that it does not matter, but it does mean that the
risk of a botched "fix" is high enough, and the problems with the
current situation comparatively small enough, that it does not merit
High or Critical priority.  Other bugs are more important.  Medium
priority is appropriate here, and that's what the bug has.

-- 
fresh Ubuntu install marks all packages as manually installed
https://bugs.launchpad.net/bugs/424643
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