Add commands to `nmdc_database_tools.py` to find, handle, and report on missing / orphan data objects and functional_annotation

[mbthornton-lbl]

Add command(s) to find and report on:

• Missing has_output Data objects for OmicsProcessing
• Missing has_input or has_output for WrokflowExecutions
• Orphan Data Objects with option to delete orphans
• Non-conforming orphan functional_annotation records