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enh: properly handle internal basins in CLI condense, repack, and com… #1063

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Run time

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Job	Run time
build (3.8, macos-12, none)	1m 38s
build (3.8, ubuntu-latest, none)	1m 27s
build (3.8, windows-latest, none)	2m 57s
build (3.11, macos-12, all)	21m 42s
build (3.11, macos-12, dcor-s3)	12m 16s
build (3.11, macos-12, none)	1m 47s
build (3.11, ubuntu-latest, all)	20m 7s
build (3.11, ubuntu-latest, dcor-s3)	8m 46s
build (3.11, ubuntu-latest, none)	1m 27s
build (3.11, windows-latest, all)	10m 30s
build (3.11, windows-latest, dcor-s3)	9m 27s
build (3.11, windows-latest, none)	2m 50s
	1h 34m 54s