Alias /flyspray /var/www/flyspray
<Directory /var/www/flyspray>
    Allow from all
</Directory>

<Directory /var/www/flyspray/adodb>
    Deny from all
</Directory>

<Directory /var/www/flyspray/conf>
    Deny from all
</Directory>

<Directory /var/www/flyspray/includes>
    Deny from all
</Directory>

<Directory /var/www/flyspray/templates>
    Deny from all
</Directory>

<Files /var/www/flyspray/plugins/*.php>
    Deny from all
</Files>

<Files /var/www/flyspray/plugins/fetch.php>
    Allow from all
</Files>