Start expanding the implementation to handle two possible converter types.  Still using the old mencoder converter, but eventually allowing for a libav converter as well.
Updated the threadly version, and did a couple of the simpler TODO notes
Updated readme and provided my personal bash script that I run as a cron for an example to others
Implementation for libav conversion.  This also detects if libav is installed, and if not defaults to the old mencoder implementation.  The libav conversion is more sophisticated.  It checks what the container format is, what the audio codec is, and the video codec is.  Copying if possible, but otherwise doing the conversion.
Updated the readme with details for what I just committed.
Make sure we compile for java 1.6
Fixes for some minor bugs in the argument checking as well as it appears we need a shell to exec in