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Add Commander-governed native RNA, DNA, and CLI spine#2

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FreshSoftware4 wants to merge 55 commits into
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chatgpt/native-core-pass1
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Add Commander-governed native RNA, DNA, and CLI spine#2
FreshSoftware4 wants to merge 55 commits into
mainfrom
chatgpt/native-core-pass1

Document native constraint core factorization

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