Having just been reading (& modifying) the command line parsing, I think that it imight be actually possible to specify multiple uploads and/or downloads on the commandline -- because they're processed (of course) in a loop.
I'm not positive, because I didn't go back and check (it might ignore them after the first transfer -- but that could probably be changed).
But, what I really had wanted was anyway recursive & wildcard support.
Of course, it could be done by doing a recursive traversal outside of FileZilla -- and then one could use real regular expressions on directories and files -- and invoking FileZilla for each file desired. That costs the connection & TLS setup for every file individually, but almost certainly leads to the most flexible solution
I like ncftp, but I've never used it for anything but plaintext ftp.
I see this in their FAQ:
Q. Does NcFTP support any secure FTP modes a la SFTP/SSL/SSH Tunnels?
A. NcFTP does not have any built-in support for encryption or secure FTP of any type. We do not support any type of interaction with hacks such as FTP over SSH tunnels. We may implement a secure FTP mode at a future date, but please do not ask for an ETA.
That sounds like ncftp is only for plaintext transmission of passwords, which I'm not interested in -- I intend to use FileZilla on multiple systems as a regular user (ie, without installing any third party or system software), and I want a transmission that at the least does not send plaintext passwords. FileZilla is nice because (among other reasons that it is nice) it can be "installed" via xcopy -- that is, you can copy the files into a user-accessible directory, and run them as that user, without ever having to solicit Admin access from the governing network staff.
I apologize, as my posts have been rushed, and I've been tired and/or not thinking clearly, and they've been somewhat unclear and not of the highest quality