ENH: `idfx clone`: include Python files (`*.py`) by default to improve support for setups that use `Pydefix` for initialization #1055

Job	Run time
Python 3.10 (isolated deps)	11s
Python 3.10 on ubuntu-latest (free-threading: false)	10s
Python 3.12 (isolated deps)	10s
Python 3.12 on ubuntu-latest (free-threading: false)	12s
Python 3.10 on macos-latest (free-threading: false)	12s
Python 3.12 on macos-latest (free-threading: false)	12s
Python 3.10 on windows-latest (free-threading: false)	32s
Python 3.12 on windows-latest (free-threading: false)	30s
Python 3.13-dev on ubuntu-latest (free-threading: false)	19s
Python 3.13-dev on ubuntu-latest (free-threading: true)	1m 10s
docs	19s
type check (3.10)	14s
type check (3.12)	12s
	4m 23s

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