FtpVC 2.6 adds the ability to move files and directories on the server. To move files and/or directories, simple select them and either use the FTP | Move command or the Move context menu command:

The Move dialog prompts for the destination directory (not that all paths are absolute, not relative), as well as allowing you to choose whether or not stubs and previous versions will be moved along with the files/directories themselves.

Press OK and the file will be moved, as shown below. Moving directories is handled in exactly the same way, except that stubs and previous versions are always moved with directories.

Note that local-only files cannot be moved, because they are not on the server to begin with.