apt-get is supposed to mark all dependencies of packages which are in
section "metapackages" as manual. This is required in order to prevent
the removal of the whole system when you remove the metapackage or one
of its dependencies (which also remove the metapackage, of course).

So I suppose some (or allmost all) packages existed on your system
before you installed kubuntu-desktop (or before apt-get got the code to
handle "metapackges" section in a special way) and as such, these
packages where not marked as manually installed.

I looked into the changelog and the code to mark as manual installed for
metapackage dependencies was integrated in 0.6.46.4ubuntu10 version on
2007-03-14 which happened during the beta stages of feisty. So if you
started from a non-beta feisty or upgraded after 2007-03-14's change hit
the archives you should not be affected.

And question to Michael. What happens when /var/lib/apt/extended_states is 
removed? Does apt-get thinks that all packages are auto or manully installed? 
I tried to rename extended_states to extended_states.dis and did "apt-get 
remove ubuntu-standard". No complaint for autoremoval was made. So I suspect 
that apt-get thinks that all packages which are not in extended_state are 
manually installed. Is it really so?

-- 
apt wants to auto-remove all my system!!!
https://bugs.launchpad.net/bugs/64814
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Bugs, which is the bug contact for Ubuntu.

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