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If a program is free software when it leaves the hands of its author, this does not necessarily mean it will be free software for everyone who has a copy of it. For example, public domain software (software that is not copyrighted) is free software; but anyone can make a proprietary modified version of it. Likewise, many free programs are copyrighted but distributed under simple permissive licenses that allow proprietary modified versions.
The paradigmatic example of this problem is the X Window System. Developed at MIT, and released as free software with a permissive license, it was soon adopted by various computer companies. They added X to their proprietary Unix systems, in binary form only, and covered by the same nondisclosure agreement. These copies of X were no more free software than Unix was.
The developers of the X Window System did not consider this a problem -- they expected and intended this to happen. Their goal was not freedom, just ``success,'' defined as ``having many users.'' They did not care whether these users had freedom, only that they should be numerous.
This lead to a paradoxical situation where two different ways of counting the amount of freedom gave different answers to the question, ``Is this program free?'' If you judged based on the freedom provided by the distribution terms of the MIT release, you would say that X was free software. But if you measured the freedom of the average user of X, you would have to say it was proprietary software. Most X users were running the proprietary versions that came with Unix systems, not the free version.