I tried to reproduce this issue with Gutsy Bibbon Tribe 5 LiveCD.

The issue regarding bogofilter vs. bogofilter-sqlite is resolved: I
enabled the Universe repository, installed bogofilter-sqlite,
uninstalled bogofilter, and checked that the proper binary is created in
/usr/bin/bogofilter, and that Evolution still works.

Anyway, the Evolution junk filtering in Gutsy is totally broken (at
least from the LiveCD). Trying to test this specific issue, I was bitten
by these bugs:

 * Gutsy installs bogofilter by default. In Evolution, under Edit ->
Preferences -> Plugins, BOTH bogofilter AND spamassassin are enabled by
default, even though spamassassin is not installed (see bug #950337)

 * Even if bogofilter is enabled in the Plugins menu, the junk filter
won't work until the user go to Edit -> Preferences -> Mail Preferences
-> Junk tab, and selects a "Default junk plugin". I think this is an
Ubuntu specific issue (see #127530). It's not very clear the double
configuration (both Plugins AND Preferences) needed to get the junk
filter working.

 * Even if there's no Default junk plugin selected in the preferences,
Evolution lets the user mark messages as junk / not-junk, which is
totally silly because it's not "learning".

-- 
Bogofilter plugin doesn't work with bogofilter-sqlite
https://bugs.launchpad.net/bugs/81581
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