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Make MD output settings optional #4221

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Job	Run time
💻-ubuntu-latest 🐍-3.10 🗃️>1 oechem: no	4h 27m 29s
💻-ubuntu-latest 🐍-3.11 🗃️>1 oechem: no	4h 4m 19s
💻-ubuntu-latest 🐍-3.12 🗃️>1 oechem: no	5h 24m 30s
💻-macos-latest 🐍-3.12 🗃️>1 oechem:	2h 29m 41s
💻-ubuntu-latest 🐍-3.11 🗃️<2 oechem:	4h 0m 53s
💻-ubuntu-latest 🐍-3.11 🗃️>1 oechem: yes	4h 7m 8s
💻-macos-latest 🐍-3.12 🗃️>1 oechem: Array	2h 45m 44s
	1d 3h 19m 44s