fix: nested directory support for wheel #3246

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Run time

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Job	Run time
Ubuntu / 3.8	56s
Ubuntu / 3.9	58s
Ubuntu / 3.10	1m 9s
Ubuntu / 3.11	56s
Ubuntu / 3.12	1m 12s
Ubuntu / 3.13	1m 20s
MacOS / 3.8	1m 30s
MacOS / 3.9	48s
MacOS / 3.10	47s
MacOS / 3.11	45s
MacOS / 3.12	45s
MacOS / 3.13	1m 15s
Windows / 3.8	2m 17s
Windows / 3.9	2m 19s
Windows / 3.10	2m 46s
Windows / 3.11	2m 44s
Windows / 3.12	2m 32s
Windows / 3.13	3m 49s
Ubuntu / pypy-3.8	2m 54s
	31m 42s