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I am not a patent lawyer, but the patent seems to imply they are patenting the API
no you can't patent an API so that you can say: "System.Collections.Stack is patended an no one can have a function called System.Collections.Stack"
This has nothing to do with patents. On software patents you cover a specific idea completely independent if you call the fuction foo or bar and completely independent if you implement this idea in C, C++ or any other language.
Some quotes from the CNet article:
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If approved as is, the patent would cover application programming interfaces (APIs) that allow actions related to accessing the network, handling Extensible Markup Language (XML), and managing data from multiple sources. APIs are the hooks in software that allow applications to work with another system.
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"It looks pretty broad," said Jeff E. Schwartz, a partner with McKenna Long & Aldridge. "It could be fairly significant."
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Meanwhile, Bruce Perens, a consultant and leader of the open-source movement, worries that Microsoft's patents could shut out alternative software development. "Microsoft is being careful to patent every aspect of APIs related to .Net," he said. "It's preventing the open-source community from being involved in this area."






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I am not a patent lawyer, but the patent seems to imply they are patenting the API (software patents are such a nightmare combination of legal and tech lingo).
In order to work around the patent I would guess you will need to completely change the API of the Mono class library, in which case you will break all compatibility of Mono with .NET (and thus the concept of "moving" .NET applications to Linux falls apart) and you will break all existing Mono apps as everyone has to rewrite to the new API.
This patent (if granted) does not seem like something that has an attractive "implement around" option, in which case you are stuck with licensing it under whatever terms MS sees fit. To me, all of this makes Mono an insane idea at this moment.