Josip Almasi

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Tried with non-profit and failed, due to issues you described so well.
But then I discovered that open source works quite well with for-profit, and last 5 years I make for living exclusively with open source.
Sometimes it's just developing custom software, which we deliver with source. More often, it's customizing free software.
If we think we have something useful to general public, we publish under GPL.
But vast majority of revenue are services based on open source, all the way from teaching to maintenance.

And what about intellectual property?
No we don't do that.
As simple as that.

So I don't think open source vs. intellectual property should be an issue for a non-profit.
Real issues are those specific to non-profit organizations, from, obviously, making no money, to volunteers who don't do what they were volunteering for.
Or, merging non-profit activities with for-profit activities may be real trouble.