A couple of months ago, I had to make a Source Code Search Engine for the SAMATE Reference Dataset. The organization of our source code are not really common but still, it's easy to understand and organized.
I now release this tiny python script in the beta section: pyIndex.

You should have all the information you need to use/adapt this script for your own purposes; it uses a MySQL database and MySQLdb to connect to the database. The script is only for adding some words or references in the database, the search is not done (but it's only a really simple SQL query...)