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Make the default stage for x.py configurable
This allows configuring the default stage for each sub-command individually. - Normalize the stage as early as possible, so there's no confusion about which to use. - Don't add an explicit `stage` option in config.toml This offers no more flexibility than `*_stage` and makes it confusing which takes precedence. - Always give `--stage N` precedence over config.toml - Fix bootstrap tests This changes the tests to go through `Config::parse` so that they test the actual defaults, not the dummy ones provided by `default_opts`. To make this workable (and independent of the environment), it does not read `config.toml` for tests.
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