Ummm.. maybe it was the way I was taught (having to enter each file name to transfer by hand back in the old DOS days), but I have never allowed my FTP program to transfer anything but what I select. Currently, I use Core FTP and like it. It's pretty much like using File Manager, and not a huge learning curve. Pretty transparent to me. I have never used any program anywhere for FTP unattended.
If you like Filezilla, why not simply copy or move the files you want transferred into a different directory that doesn't include any files you don't want transferred? Takes just a few seconds, really. (I have only used Filezilla a few times and didn't really bond with it, sorry)
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