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Yeah: I'm pretty unhappy with the choice I made here... and with the options available. I'd like to use rustfmt for formatting so that the generated code could pastt cargo fmt... but it's not feasible to use it as a library and shelling out has many problems--including the one you've noted. At this point, I'm inclined to switch everything over to prettyplease and see if that's a better experience. PRs welcome or I'll try to get to it in the next week or two.
The formatting options used by the cargo install version (https://github.com/oxidecomputer/progenitor/blob/main/cargo-progenitor/src/main.rs#L94) use formatting options that are documented as unstable:
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