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feat: Add unified CLI for run_guidance and fix missing args bug #32

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Run time

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Job	Run time
lint	1m 37s
tests (boltz-dev)	2m 29s
tests (protenix-dev)	4m 2s
typecheck (rf3-dev)	1m 29s
typecheck (protenix-dev)	1m 42s
typecheck (boltz-dev)	1m 39s
tests (rf3-dev)	1m 45s
	14m 43s