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I'm still a little confused about whether Cyberduck supports compression over SFTP (as in rsync -z). Do you have to use either SFTP or SCP mode to get this to work?
Fugu has a checkbox for this for each connection. Even if it does, the user interface could better clarify this with a "compression" checkbox under "More Options" in the "Open Connection" window.
Of course there are times when this compression is desirable and times when it isn't, so a per-connection setting would be really handy.
SFTP in Cyberduck does not make use of compression which results in slower transfers than command line sftp with the -C option.
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