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use "Ignore Folder Structure: option in command line
Not directly in script. However, you can configure a blank, new saved Folder Compare session with the option set, then load it as a base level of settings. You can then load folders into it:
Maybe I'm wrong but I think it's a good practice to add "switches" before "parameters". Also the man page of rsync reports --exclude usable as with the "=" syntax or without. So to standarize across operating systems, I'd use rsync -av --progress --exclude="thefoldertoexclude" sourcefolder /destinationfolder - anyway upvote for the rsync instead of the find, as you can easily use absolute paths for the source while in the find it's trickier as it uses the {} in the dst.
Expanding on our arguments and script options is something on our wishlist. We just don't currently have the "Ignore Folder Structure" flag, but do load all options when loading a session, so loading the session is the workaround. We also have a list of command line options, but generally our script is multiplatform, too, as well as passing in any text variables from the command line that can insert into scripting.
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