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feat: Add unified CLI for run_guidance and fix missing args bug #33

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Run time

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Job	Run time
tests (rf3-dev)	1m 59s
typecheck (rf3-dev)	1m 2s
tests (boltz-dev)	2m 5s
lint	1m 19s
tests (protenix-dev)	3m 40s
typecheck (boltz-dev)	1m 5s
typecheck (protenix-dev)	1m 18s
	12m 28s