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Right now metamath-exe never actually writes .mm files itself. This makes it difficult to implement things like save proof * /compressed or comment rewrapping, which is one of the essential functions of metamath-exe. Tools that generate proofs also want to be able to construct mm snippets, and whole file refactors like theorem renaming or inlining require editing a .mm file, not just generating one from scratch (if we want to minimize the diff). Metamath-knife is well positioned to do these things, and to some extent it was designed for this with "incremental mode" support, but there is still some work to be done to make it actually work and have a useful API.
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