The behavior displayed in the bug report matches the description in the
manual page quoted in comment 4, notably:

> mark all freshly installed packages as automatically installed

As such, the --mark-auto option does not affect packages which are
already installed, and they are subject to the usual rules:

If an upgrade is available, it is installed and the state is unchanged.
Otherwise, the state is set to manually installed.

Personally I'm not convinced that the state change is correct in any
case, but there's arguments for both sides. In particular I am worried
that users accidentally end up marking a lot of packages as manually
installed that they did not intend to.

Whether the mark-auto flag should apply to already installed arguments
is a topic that I have not formed an opinion on so far. Needless to say
changing an installed package from manual to auto because you pass it to
--mark-auto is not going to be the right call in most places, and we're
talking really about the issue entirely independent of mark-auto.

** Changed in: apt (Ubuntu)
   Importance: Undecided => Wishlist

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https://bugs.launchpad.net/bugs/2100937

Title:
  apt install --mark-auto does not retain auto mark

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