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I was having a heck of a time getting pretty permalinks to work with this site.  I figured it had to do with setting up WordPress in its own directory, which I had done using their own instructions (http://codex.wordpress.org/Giving_WordPress_Its_Own_Directory). In the end it turned out I was right.  My .htaccess file that I copied into my root web directory looked good, but I needed to turn on Apache’s AllowOverride setting.  After some snooping around on my Ubuntu 12.04 machine, I finally discovered where to make this change.  In the /etc/apache2/sites-available directory, I had to update the file called default.  There was a configuration section in it for the /var/www directory and changing “AllowOverride None” to “AllowOverride All” did the trick!