Although I can't find any documentation--they haven't yet written the updated version for the ini file format (as of 2014-05-01): https://github.com/hhvm/hack-hhvm-docs/issues/156
Regardless I figured it out and they confirmed it should be:
hhvm.server.file_socket=/var/run/hhvm/hhvm.sock
It looks like you take the camel case command line argument -vServer.FileSocket
and drop the v, lowercase it, split it with underscores instead of camel case.
If y ou follow the above rewrite rules you can convert the old format to the new.