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I can't figure out what would be the best way to do this with FtpVC. Is there a way to keep track of our own internal numbering scheme for versions or does it have to done by filename or directory name? I noticed FtpVC does it's own default version numbering (1,2,3... ) without anywhere that I can see to override it.
No, FtpVC doesn't allow users to control version numbers -- they are simply incremented after each check-in. This is pretty common in version control systems.