BUG (clone): fix an issue where cloning to a dir with missing parents might create orphan empty directories if the atomic copy failed #1072

Job	Run time
Python 3.10 on ubuntu-latest (free-threading: false)	15s
Python 3.10 (isolated deps)	15s
Python 3.11 on ubuntu-latest (free-threading: false)	11s
Python 3.12 (isolated deps)	10s
Python 3.12 on ubuntu-latest (free-threading: false)	15s
Python 3.10 on macos-latest (free-threading: false)	17s
Python 3.11 on macos-latest (free-threading: false)	12s
Python 3.12 on macos-latest (free-threading: false)	13s
Python 3.10 on windows-latest (free-threading: false)	34s
Python 3.11 on windows-latest (free-threading: false)	45s
Python 3.12 on windows-latest (free-threading: false)	29s
Python 3.13-dev on ubuntu-latest (free-threading: false)	21s
Python 3.13-dev on ubuntu-latest (free-threading: true)	1m 36s
docs	18s
type check (3.10)	13s
type check (3.12)	12s
	6m 16s

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