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I have a complete copy of my entire web server on my local hard disk. In earlier versions of Cyberduck, I could just synchronise the server root with my local directory, and the changed files would be uploaded without trouble.
The version of Cyberduck I use now (most recent) only synchronises the files in the top server directory - and it does so regardless of whether those files have been modified at all. A modified file in a subdirectory however is not synchronised.
I have marked this as major since it's far beyond "normal" to manually upload changed files when you actually have a synchronisation feature that is supposed to be working properly.
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I'm finding new files are recognised and uploaded in subdirectories, it's only altered files that are not.
Also, the files in the top directory are listed, but they're not actually being downloaded/synchronised regardless (and the up/down arrows previously present are not) for me at least.
i just checked using the latest nightly Version 2.8b1 (3223) after it failed to work with the newer 'official' release.
Synchronise is still not mirroring modified files. New files up/download fine. But all files present both locally and remotely, while all now showing up, are now un-checked and greyed out, even if they are different size/have different timestamps (this is even recognised by cyberduck in the 'details' part). Ticking the box seems to have no effect.