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The second right-click option: Add books from directories, including sub-directories (One book per directory, assumes every ebook file is the same book in a different format)
I always assumed was specifically there to rebuild a Saved To Disk calibre library. After all, it is not recommended to use the same metadata.db on both windows and linux, so this is the only way to safely share a library between the two.
I can confirm that if you use this option, it reads all the metadata from calibre's generated metadata.opf during the Save To Disk. (Or even if you need to build from the actual library used on a different OS. I tried using the library folder of a Ubuntu installation on a Windows computer once but couldn't link to half my ebook files until I rebuilt from the library folder into a new library.)
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