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Closes https://github.com/denoland/deno/issues/25321
Ended up being a larger refactoring, since we're now juggling
(potentially) two config files in the same `add`, instead of choosing
one. I don't love the shape of the code, but I think it's good enough
Some smaller side improvements:
- `deno remove` supports `jsonc`
- `deno install --dev` will be a really simple change
- if `deno remove` removes the last import/dependency in the
`imports`/`dependencies`/`devDependencies` field, it removes the field
instead of leaving an empty object
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