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I use MobSync to sync podcasts. I'll have to check my MobSync setup.
I use iPodder to d/l the podcasts I want into a "folder#1" and use MobSync to sync all the files from "folder#1" into a "My Podcasts" folder in /My Documents.
So, I believe its just individual files from a folder. But I believe you can set multiple different "jobs" so MobSync can sync between other folders as well. I don't think you can sync the folder itself.
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