makefile cleanup: identify out-dated code; extract todos into issues

[turbomam]

remove some of these scripts?

oak-tree-to-pv-list = "nmdc_submission_schema.scripts.oak_tree_to_pv_list:main"
dh-json2linkml = 'nmdc_submission_schema.scripts.dh_json2linkml:update_json'
linkml-json2dh = 'nmdc_submission_schema.scripts.linkml_json2dh:extract_lists'

• use fewer enums? is that really desirable or even possible?
• use booleans for yes/no enumerations? what would the benefit be?
• check for numbers that appear as strings in the schema (just examples? check for minimum value etc)
• check if maximum value for pH has to be an int?
• RDF/TTL generation is failing https://github.com/microbiomedata/submission-schema/issues/13

old hints for alternate import sources in pyproject.toml:

• /Users/MAM/Documents/gitrepos/sheets_and_friends
• home/mark/gitrepos/sheets_and_friends
• sheets-and-friends = { path = "/home/mark/gitrepos/sheets_and_friends", develop = true }

[turbomam]

removing these yq commands that had previously been commend out

#   yq -i '(.slots.[] | select(has("range") | not  ) | .range ) = "string"' $@
#   yq -i '(.classes.[].slot_usage.[] | select(has("range") | not  ) | .range ) = "string"' $@

#   yq -i '(.slots.[] | select(.name == "dna_dnase") | .range) = "boolean"' $@
#   yq -i '(.classes.[].slot_usage.[] | select(.name == "dna_dnase") | .range) = "boolean"' $@