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[rant]
Sure, but it's the same thing -- you lose package management for when you want to uninstall (or query file / package relationships)
Since you have to apt-get uninstall calibre first, you also end up with "orphaned" dependcies, which means apt "helpfully" prints
The following packages were automatically installed and are no longer required: ...
... every time you use it.
I guess it's not a big deal for a single package, but once you start making exception after exception the filesystem gets pretty messy.
Of course, it's quite surprising that some popular (and high quality) packages are so neglected by Debian. It sometimes looks like the maintainer has pretty much abandoned the package without formally giving up maintainership.
[/rant]
Anyway, thanks to all who replied.
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