Change how directories and symlinks in directories are handled when r… #12723

Job	Run time
Linux package	12m 30s
Bundle test (ubuntu-latest)	2m 5s
Linux (python=3.10 cc=gcc sanitize=0)	2m 13s
macOS Brew	4m 10s
Bundle test (macos-latest)	3m 58s
Test ./dev.sh and benchmark	1m 37s
Linux (python=3.12 cc=clang sanitize=1)	2m 35s
Linux (python=3.11 cc=gcc sanitize=1)	2m 14s
	31m 22s

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