Richard,
What constitutes a comment varies from file-format to file-format. The
APT preferences file format does not have any syntax for comments. It
does allow lines beginning "Explanation: " followed by freeform text,
but only immediately preceding a "Package: " line, so they aren't really
comments, really.
It's not unreasonable for APT to complain loudly if one of its config
files contains a syntax error, which #-marks are in this context.
** Changed in: apt (Ubuntu)
Status: New => Incomplete
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comments in /etc/apt/preferences make it break
https://bugs.launchpad.net/bugs/348729
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