Centralize --validation-mode and --skip-validation #2933

Job	Run time
pyright	19s
mypy	54s
pathogen-repo-ci (dengue)	2m 39s
test (python=3.8 biopython=1.80)	11m 50s
pathogen-repo-ci (lassa)	55s
test (python=3.8 biopython=latest)	11m 22s
pathogen-repo-ci (measles)	1m 20s
check-docs	37s
test (python=3.9 biopython=1.80)	12m 49s
pathogen-repo-ci (mpox)	1m 23s
test (python=3.9 biopython=latest)	12m 34s
pathogen-repo-ci-v0 (avian-flu)	53s
pathogen-repo-ci (seasonal-cov)	1m 59s
test (python=3.10 biopython=1.80)	12m 26s
pathogen-repo-ci-v0 (ebola)	54s
pathogen-repo-ci (zika)	58s
test (python=3.10 biopython=latest)	12m 58s
test (python=3.11 biopython=1.80)	12m 34s
pathogen-repo-ci-v0 (mumps)	1m 5s
test (python=3.11 biopython=latest)	12m 50s
pathogen-repo-ci-v0 (ncov)	1m 8s
pathogen-repo-ci-v0 (rsv)	8m 29s
pathogen-repo-ci-v0 (seasonal-flu)	1m 19s
pathogen-repo-ci-v0 (tb)	1m 14s
build-docs / build	2m 17s
codecov	35s
release	0s
rebuild-docker-image	0s
	2h 8m 21s

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