The MP3 Factory: 'De-borking' MP3s on Linux page was update a bit, but more importantly i released v0.4a of MP3 Factory. This version addresses what may have been a critical bug that could potentially lead to files outside of the script directory being deleted. Other changes include a better 'tag to file name' operation experience and many other smaller improvements and polish.
Note that this version is largely untested. I know the convert to MP3 and tag to file name operations are working, but i didn't do much testing with anything else, though all operations should be working. I wanted to get the 0.4a release up ASAP to address the nasty bug i found.