It is going to be the replacement for NTFS on Windows. It was supposed to be part of the Longhorn release, but they just decided to untie WinFS from Longhorn. WinFS will arrive after Longhorn, so that we can actually get Longhorn in 2006.
Technically, they are rebuilding the underlying mechanisms that the OS uses to find and store data on a disk. I'm no NTFS expert, but I assume it is based on table lookups, just as FAT and FAT32 were. WinFS will instead be based on a relational database, i.e. they are going to embed a SQL Server desktop engine into our OS. Why? Allegedly this will make it easier for us to find files and such, no matter where they are on the drive.
A noble idea, but worthless IMHO. We can do that pretty easily already if the files have metadata attached (e.g. adding a title or comments to your Word docs or picture files). Switching over to a relational DB on the back end does not remove our obligation to populate this metadata, but no one does it. Only MP3 files seem to be well populated, and that's only because ripper programs can all hit CDDB or freedb to do the work for us! So although WinFS is an unstoppable force (all Windows users will be on it sooner or later), I don't see it as any sort of panacea.
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Updated June 21, 2019