Remove use of ncov-ingest geolocation rules

[joverlee521]

Once augur curate apply-geolocation-rules uses built-in default rules (nextstrain/augur#1744 + nextstrain/augur#1745), we can remove the use of ncov-ingest geolocation rules from pathogen ingest workflows.

TODOs

Based on GitHub search

We can prioritize updating the pathogen-repo-guide, docs, zika, and mpox

• ingest: Remove use of ncov-ingest geolocation rules pathogen-repo-guide#81
• creating-an-ingest-workflow: Remove use of ncov-ingest geolocation rules docs.nextstrain.org#242
• ingest: Remove use of ncov-ingest geolocation rules zika#79
• ingest: Remove use of ncov-ingest geolocation rules mpox#303

Other pathogens can be updated later as needed

• avian-flu
• dengue
• hmpv
• lassa
• measles
• nipah
• norovirus
• oropouche
• rabies
• rsv
• rubella
• WNV
• yellow-fever

[jameshadfield]

Other pathogens can be updated later as needed

Once the new version of Augur is out, will these at least need to use --no-default-rules, or will they be OK because their custom rules will essentially include the default rules as they fetch (a similar version of) the defaults and use them as custom rules?

[joverlee521]

Other pathogens can be updated later as needed

Once the new version of Augur is out, will these at least need to use --no-default-rules, or will they be OK because their custom rules will essentially include the default rules as they fetch (a similar version of) the defaults and use them as custom rules?

They should be okay because their custom rules still include the ncov-ingest rules that will override the default Augur rules.