If one makes any changes, adds files, moves files in a repo while Codex CLI is working, as “clean up” Codex will restore those files to the previous commit. It’s repeatable and it does it every time.
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Can you let it work in its own branch and then make PR with the udpates? There’s definitely a multi-user challenge associated with any large software team… automated coders can make this worse if you don’t use best practices. Working in separate branches, you can have several automated agents working against the same code base at the same time, just like you might have many people working, with reconciliation through pull requests.
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I think this is what microservices are needed for.
I have build a special framework for myself that enables multiple bots to work on the same codebase in parallel.
In fact I am still working on an open source version of it.