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Ah, I missed the undocumented working_dir in fig.yml. That will be useful! I just found myself looking for the command line switch a few times recently when debugging my container setups.
I'm generally in favour of supporting command line overrides for things in fig.yml, as long as the defaults don't require you to pass any specific command line flags.
While the current parameters for fig run (-d, -T, --rm, --no-deps) make sense to me as things you might want to change at runtime, I'm struggling to think of a common use case where you'd want to override the working dir without just going into fig.yml and changing it.
For that reason, I think I'm -1 on merging this, since the logical extension would be to support absolutely every docker run parameter, and that'll involve a lot of glue code.
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Just wired up the ability to set the workdir when using fig run.