BOINC is free software (distributed under the terms of the GNU LGPL). It can be used to only run free software or not (the user chooses the project she wants her computer to work on).

I believe my analogy with Abrowser (free software), which can run (or not) proprietary Javascript, is valid. If you want another one, there is the ScummVM precedent. This virtual machine "is almost entirely used for the purpose of running proprietary software" (according to the original description of the issue) and yet still is in Trisquel 6.0's repository because it is free software and can be used to run free software games.

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