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I think codex has done something along the line: https://github.com/openai/codex/pull/6041

But it is trying to use git as a backend to save file states, and at the same time NOT showing it in the user's git history.

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I haven't tried it, but conceptually I can imagine that it is good to have a separate VCS for the agent. This way I can keep git clean and easy to understand for humans and still keep all the verbosity the agent needs.
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> This way I can keep git clean and easy to understand for humans

Personally I like it best when both humans and agents find it clean and easy to understand, but we all like different things :)

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Branches and worktrees exist and can effectively act as a "separate" history. At the end of the day you would still merge the changes in, possibly with a squash if you don't care about the little commits.
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It's really not. Anything the LLM can benefit from people can too. Keeping minimal explicit information in git history is a cultural norm not proven best practice. The best codebases I've worked on have very large commit messages and searching them is very useful. We should have been doing it that way all along.
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