Rework of `mila init` following changes #979

Job	Run time
Run linting/pre-commit checks	29s
unit-tests (ubuntu-latest, 3.10)	1m 40s
unit-tests (ubuntu-latest, 3.13)	1m 38s
unit-tests (ubuntu-latest, 3.11)	1m 40s
unit-tests (macos-latest, 3.10)	1m 39s
unit-tests (windows-latest, 3.10)	1m 39s
unit-tests (windows-latest, 3.9)	1m 39s
unit-tests (windows-latest, 3.13)	1m 39s
unit-tests (ubuntu-latest, 3.9)	1m 33s
unit-tests (windows-latest, 3.12)	1m 39s
unit-tests (windows-latest, 3.11)	1m 39s
unit-tests (macos-latest, 3.9)	1m 39s
unit-tests (ubuntu-latest, 3.12)	1m 37s
unit-tests (macos-latest, 3.11)	1m 38s
unit-tests (macos-latest, 3.12)	1m 38s
unit-tests (macos-latest, 3.13)	1m 38s
integration tests with a real SLURM cluster	0s
Upload coverage reports to Codecov	-1s
	25m 3s

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