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🐛 fix(config): prevent env_run_base deps from being clobbered #1569

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Job	Run time
tox env dev on ubuntu-24.04	38s
tox env dev on windows-2025	31s
tox env docs on ubuntu-24.04	28s
tox env type-min on windows-2025	32s
tox env docs on windows-2025	32s
tox env type on windows-2025	32s
tox env type-min on ubuntu-24.04	33s
tox env pkg_meta on windows-2025	32s
test 3.13 on macos-15	33s
test 3.12 on macos-15	43s
test 3.10 on ubuntu-24.04	32s
test 3.13 on windows-2025	32s
test 3.11 on windows-2025	32s
tox env type on ubuntu-24.04	29s
test 3.12 on windows-2025	31s
test 3.14 on ubuntu-24.04	41s
tox env pkg_meta on ubuntu-24.04	1s
test 3.11 on macos-15	31s
test 3.12 on ubuntu-24.04	41s
test 3.14 on windows-2025	1s
test 3.14 on macos-15	15s
test 3.11 on ubuntu-24.04	41s
test 3.13 on ubuntu-24.04	29s
test 3.10 on windows-2025	32s
test 3.10 on macos-15	1s
	12m 3s