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I’ve just mailed Sarabian a bit of advice on how I set up Pyblosxom websites. Note that this is probably pretty specific to me, but I present the advice below anyway in case it’s useful to someone else:

/var/www/example.org
                    /html
                         /pyblosxom
                                   /pyblosxom.cgi
                                   /config.py
                                   /.htaccess [1]
                    /pyblosxom
                              /Pyblosxom [2]
                    /plugins [3]
                    /sites
                          /blogging-hacks

<Files config.py>
deny from all
</Files>

[2] This is the Pyblosxom distribution
[3] Put all your plugins in here

RewriteRule /weblogs(.*) /pyblosxom/pyblosxom.cgi$1

and then it should all work.