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Github praises open source but they sure do keep their own stuff as proprietary as possible. (Even their EE is obfuscated code)

None of the extra data (issues etc) is stored in git. However they do have a comprehensive HTTP API, so one can migrate away using that.

Question: is all the auxiliary project data (issues, etcetera) also stored in the git repository, or is that data stored separately by github (and thus impossible to migrate out of it)?

Separate. You can fetch most of issues and so on as long as 1) GitHub does not change its policy 2) You have an account 3) The project has not been deleted or somehow locked

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