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The deal signed in the United States by the non-profit Protocol Freedom Information Foundation was focused on helping Samba, a non-profit maker of free, open source server software.
"The agreement allows us to keep Samba up to date with recent changes in Microsoft Windows, and also helps other Free Software projects that need to interoperate with Windows", said Andrew Tridgell, creator of Samba.
Microsoft In Open Source Deal [reuters.com]
"As Samba is not commercial and could not be forced out of the marketplace it was still standing and able to benefit from the ruling."
The key sentence is "As Samba is not commercial..."
Samba becomes commercial when distributed by companies such as Hewlett-Packard, RedHat, IBM, etc.
HP released a product in 2000 called CIFS/9000 based on Samba.
No wonder Gary Campbell from HP wrote a memo in June 2002 titled "Microsoft Patent Cross License - Open Source Software Impact", see [linux.com...] .
HP and Microsoft agreed on a new patent cross license in 2002. However, Campbell wrote "major products are explicitly called out as not protected by the cross license, such as Samba, Wine, KDE, Gnome, Apache, Sendmail, and Linux."
Campbell also wrote: "Microsoft could attack Open Source Software for patent infringements against OEMs, Linux distributors, and least likely open source developers. They are specifically upset about Samba, Apache and Sendmail. We believe Samba is first..."
Again, things change when open source software goes commercial and people begin to make money (profits) out of other people's patents, protocols and intellectual property.
It's good news for interoperability, even if this is on a limited scale. However, the downside is that it helps bolster proprietary protocols over open equivalents. MS gains that advantage at least, which is why it has never seriously threatened Samba in the past.