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The main problem I see with the directory based sync method is problems with the metadata.db file. Basically, you can only have a metadata.db file from one library or the other at a time. Now this isn't much of a problem if both libraries are always in sync right from the beginning. However...
What happens when you start off with only having one calibre library. You then go away with your laptop for a couple of weeks, and while you're away you start a new libary on your laptop. This new libary may include SOME books that are in the main library, and some books that are new. When you get home, you want to add the new books into the main library. But how would you do this using directory based syncing...?
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