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WinFS uses a relational database engine to make it easier for users to search their PCs and corporate networks for related files, documents and e-mail messages.
Analysts said this will reduce the value of the next Windows operating system, and make Windows XP SP 2 a better choice for business users.
The absence of WinFS could mean that Longhorn becomes a minor operating system refresh.
Jim Allchin, group vice-president of the Platforms Group at Microsoft, said, "We have had to make some trade-offs to deliver the features corporate customers, consumers and OEMs are asking for in a reasonable timeframe."
Microsoft will make WinFS available after the Longhorn release, but no date has been set.
Longhorn still includes two other new technologies: Avalon, a graphics subsystem; and Indigo, a web services-based communications architecture. These will also be released in 2006 as a subset of the Longhorn WinFX developer interface, for Windows XP and Windows Server 2003.
Neil Macehiter, research director at Ovum, said, "WinFS offers some potentially powerful capabilities and the value of the operating system as a whole is reduced with its absence.
"WinFS is potentially beneficial to users because it provides a more sophisticated, [relational database] approach to storage management. It allows users to associate their own metadata - data about data, such as author or subject - with data stored by the operating system, making it easier to search, navigate and relate.
"This will also come as a personal blow to Bill Gates, for whom the storage facilities promised by WinFS have become a 10-year and still-elusive holy grail. Clearly, the desire to get out the software in 2006 has required compromise at the highest levels of the company," Macehiter said.
Gartner said in an alert last week that it considered Longhorn to be a logical upgrade from Windows XP. It advised companies to standardise new PCs on Windows XP SP 2.
It added that users should not make strategic plans based on the immediate availability of WinFS.
"When Microsoft offers more information on the timing, delivery mechanism, upgrade process and benefits of Longhorn and WinFS, those running XP will be using an up-to-date, fully supported OS, and will be able to choose between adopting the first Longhorn release and waiting for the release that includes WinFS," said the alert.
Gartner said most users will run some version of Windows XP through to 2011, and that most Windows servers in 2010 will still run Windows 2003 Server.
For companies using Windows 2000 and older operating systems, Macehiter said the question of whether to upgrade "depends on the exact requirements and issues faced by particular users. However, they need to consider the potential value of the offering in the light of their requirements".
Microsoft plans the first beta of Longhorn for the second half of next year.