Update pathogen repos to conform to smart pathogen-repo-ci

[joverlee521]

See #84 for context, follow up on #89

Update pathogen repos to use the latest version of the pathogen-repo-ci. We can start with the pathogens that have already been "modernized". Other pathogen repos should have been pinned to an older version of the pathogen-repo-ci as part of #93.

Searched for Nextstrain repos that are currently using pathogen-repo-build as their CI.yaml workflow with https://github.com/search?q=org%3Anextstrain+%2Fpathogen-repo-build%5B.%5Dyaml%40%2F+path%3A**ci.yaml&type=code

• dengue
• measles
• mpox -> Switch CI to pathogen-repo-ci action [#257] mpox#258
• zika