The two companies signed interoperability and distribution agreements as well as a patent covenant that protects users of Novell's SuSE Linux distribution against intellectual property claims from Microsoft.
The patent agreement goes against the ideals of the free software movement to which Moglen subscribes.
Headed up by GPL creator Richard Stallman of the Free Software Foundation, its supporters believe that all software should be available free of charge and without any patent threat.
By charging Novell a fee for its intellectual property, Microsoft is effectively forcing Novell Linux users to pay Microsoft for the software.
Novell has provided Moglen with confidential access to the legal details of the deal between the two companies.
A spokesman from the Software Freedom Law Center said that the audit had been completed, but could not comment on its findings.
According to a report by Reuters, Moglen is now planning to close the loophole that allows Microsoft to charge Novell for distributing the software in the forthcoming GPL3.
The Linux operating system kernel is governed by the GPL2, and the project plans to stay under that licence. Other open source projects, however, are expected to switch to the GPL3 once it comes out.
Novell's SuSE Linux distribution bundles multiple GPL applications. The Linux vendor will no longer be able to distribute any of these if they switch to the GPL3.
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