I spent a little time with the search function at A2A, and found this:
http://www.a2asimulations.com/forum/viewtopic.php?f=10&t=6596&p=55683#p55683these details ought to have made it into the manual, but didn't. ms files are
the files that control the selection of appropriate skin. Apparently the fx
files add lighting effects to the aircraft surfaces. It is also possible to
fully enable multiskin but edit the .ms files to only use one skin, but still
provide individual lettering for all aircraft. This gives even more multiskin
features for machines that can't cope with all the texture files (these days
ought to be at least 512MB vidRAM). Details here:
http://www.a2asimulations.com/forum/viewtopic.php?f=48&t=23195