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Already fixed.
yes
maybe, depends on the pdf in question.
yes
when you add books from the kindle, collections are not migrated to calibre (since they are not part of book metadata). Use the tags for this. Though really since tags (or collections) are many valued, there's no good way to automatically convert them into a folder hierarchy
Feel free to open an enhancement ticket, but I'm not overly motivated to do this. It's error prone and messy and I personally would never use the collections feature on a Kindle anyway.
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