Exclude SPM checkouts form indexing, closes #809 #1265

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Run time

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Job	Run time
Lint	10s
Linux (6.0-nightly)	3m 27s
macOS (16.1)	4m 23s
Linux (5.10)	2m 32s
macOS (15.4)	3m 14s
Linux (5.9)	2m 34s
macOS (15.2)	3m 34s
	19m 54s