@PHPn00b and @btm, I'm aware of two methods to publish project files. I use Subversion to manage revisions and to checkout updates on my production server and am very happy with the flexibility and power using version control provides.
@ragaskar commented on the RSE Eclipse plugin which might open up the possibility of publishing files from the command line via scp or ftp.
There may be other file publishing plugins that provide what you're looking for.