Use `ExtendOverwriteDefault` for all multi-value options #3176

Job	Run time
mypy	1m 0s
pathogen-repo-ci (dengue)	2m 47s
pathogen-repo-ci-v0 (avian-flu)	51s
check-docs	46s
pathogen-repo-ci (lassa)	7m 37s
pathogen-repo-ci-v0 (ebola)	1m 6s
pathogen-repo-ci (measles)	1m 21s
pyright	14s
pathogen-repo-ci-v0 (mumps)	1m 2s
pathogen-repo-ci (mpox)	1m 17s
pathogen-repo-ci-v0 (ncov)	1m 7s
pathogen-repo-ci (oropouche)	1m 19s
test (python=3.9 biopython=1.80)	12m 56s
pathogen-repo-ci-v0 (rsv)	8m 33s
pathogen-repo-ci (rabies)	2m 25s
test (python=3.9 biopython=1.82)	13m 0s
pathogen-repo-ci-v0 (seasonal-flu)	1m 8s
pathogen-repo-ci (seasonal-cov)	1m 27s
pathogen-repo-ci-v0 (tb)	1m 19s
test (python=3.9 biopython=latest)	13m 3s
pathogen-repo-ci (wnv)	1m 7s
test (python=3.10 biopython=1.80)	13m 44s
pathogen-repo-ci (yellow-fever)	4m 30s
test (python=3.10 biopython=1.82)	13m 49s
pathogen-repo-ci (zika)	1m 10s
test (python=3.10 biopython=latest)	13m 59s
test (python=3.11 biopython=1.80)	13m 31s
test (python=3.11 biopython=1.82)	14m 10s
test (python=3.11 biopython=latest)	13m 59s
test (python=3.12 biopython=1.82)	20m 46s
test (python=3.12 biopython=latest)	20m 21s
build-docs / build	2m 33s
codecov	16s
release	0s
rebuild-docker-image	0s
	3h 28m 13s

Provide feedback