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2.2 Since the MEX interface allows plugins to be distributed under terms that are incompatible with the GPL, does this mean that you are encouraging people to to write non-free software for Octave?

No. The original reason for implementing the MEX interface for Octave was to allow Octave to run free software that uses MEX files (the particular goal was to run SundialsTB in Octave). The intent was to liberate that software from Matlab and increase the amount of free software available to Octave users, not to enable people to write proprietary code for Octave. For the good of the community, we strongly encourage users of Octave to release the code they write for Octave under terms that are compatible with the GPL.

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