<p>In our project we have a large number (hundreds) of FLA files created by the artists in CS3, from which we compile SWFs to use in our Flex/AS3 application.</p>

<p>As part of a streamlined build/deploy system, it would be really handy to be able to automate publishing all these FLAs, and ideally deploying the SWFs too. I found some ways to do the batch publishing from CS3 using JSFL, but was surprised to discover CS3 doesn't apparently have any command-line functionality for this?</p>

<p>This is on a Linux system for what it's worth, I don't have experience with JSFL to know if you can run scripts from the command line somehow?</p>

<p><strong>note</strong>: I should have said "Linux is preferred"... I don't use Linux but our server/build PC is Linux... I didn't realise CS3 was not compatible so I guess we can do this part on Windows.</p>

How you are running Flash CS3 on Linux ? 
you cannot run JSFL from command line but compiling a FLA file should be possible
some old example
http://www.mikechambers.com/blog/2003/11/01/flashcommand-flash-2004-command-line-compiler/
newer stuff from Mike Chambers
http://code.google.com/p/flashcommand/
for OSX
so it's definitely possible seems only through semi automated IDE publishing,
too bad Flex compiler is not capable of such a thing, together with ANT tasks it's a killer...
with FDT editor things are pretty cool and automated