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That seems like an overly simplistic view of what code is, and what code can be.

It's the opposite of simplistic.

I believe the developer's constitutional rights were violated and I would contact the EFF and ACLU for help.

For some context, at one point:

> the US government designated encryption software as a "munition"

Free speech has limitations. If code is speech, then don’t those limitations also apply to code?

I'm pretty sure books have been protected by copyright too for a while now.

Not to confuse the point, this is about your right to publish your own code.