I've made a first pass at a library that you can use to talk to Indigo from a perl script. I don't know if there are any perl hackers around here but hopefully someone finds this useful. There are still several TODOs in here so I'll post an update when I get around to it.
Currently this package will take care of all the low-level stuff, i.e. socket IO and XML parsing. I will probably add a higher level layer to deal with a few common types of operations, such as toggling lights and querying things. In the mean time you will need to request the protocol info from Matt, because you will need to create those data structures in your program. I've included one example which turns on a light.
Download here: http://www.seanadams.com/indigo/
Let me know if you have any questions!