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When downloading files from a site, the entire site is automatically selected regardless. What would be more beneficial and would save considerable resources would be if only the files which are different on the server to those locally, were selected to be downloaded, as is the case with uploads.
For upload it's easy because traversing local disk structure is usually quite fast. Unfortunately, this is not the case for a remote server, it could take ages...
What information is gathered when getting the file list? It doesn't have to be perfect, but even a check of last modified & file size would do to prevent files which have been untouched for months from being downloaded every time as it is normally quicker than individually unselecting each file. Another solution could be to do the check when starting the download, and to skip it if the same. Similar to FileZilla with it's pop-up dialogue box asking to overwrite. Anything to speed up the update.
*** This bug has been marked as a duplicate of bug 176121 ***