I use Cirrus to back up my iptables config. I configured a username for Cirrus on my Linux firewall, configured a command alias for iptables so I get more info (iptables -L -n --line), and created a custom Device Type which has my command in it (iptlist). Recently, I've modified my command alias to include ip6tables, so my new alias looks like this: iptables -L -n --line && ip6tables -L -n --line. Seems to work fine, although, I do remember having trouble logging in initially because of the prompt character. I believe Cirrus had trouble parsing '$' at the end of my prompt, so I had to change it to '#'.
There should be no reason you can't include a perl or shell script that simply runs a 'cat' on several config files at once upon login, so that way you can track changes to practically any config file. The only problem with this is that all configs will be in one 'file' with regard to Cirrus. I have a feature request for Cirrus to be able to track alternate command output, such as 'show version' and 'show flash' (a. la RANCID), but I'm not sure if that's even on the road map.
FYI, providing the ability to track command output other than running and startup configs is a feature we are considering for a future release.
Also interested in this... been quite a while now.. any progress?