(Old summary: warn users to 'clear' transfer window or else significantly speed transfer window loading)
When the transfer window has several hundred items, Cyberduck hangs and slows the entire computer when loading the transfer window. This lasts more than a minute (up to 5 minutes or more for some).
This can be solved by pressing "Clear" in the transfer window, but there is no way for a user to know that this is the solution to the slowdown.
Incidentally, 'clearing' the transfer window can also take forever if there are several hundred items. I waited 30 minutes before force-quitting Cyberduck. It seems that manually selecting and scrolling items and 'removing' them causes no such delay.
My suggestion is to either considerably speed the loading of the transfer window so there is no visible delay, or else somehow warn the user to clear the transfer window when the window gets to a certain size (e.g. 50 items). But I don't see why it should take a long time to load the window. It's merely a list of things, right?
Note: I haven't confirmed this behavior on newer versions of Cyberduck (using Version 2.4b2).
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Another option is to give the transfer window a maximum size. The oldest items will start getting deleted when the maximum size is reached. The maximum can be set in the Cyberduck preferences. The default can be set at 40. 'No maximum' can also be an option for 'power users.' :)