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I've been experimenting with base pkg on FreeBSD-15 and hit this issue:
pkg info | grep metapackage
Then for each metapackage I executed:
pkg delete -f FreeBSD-set-XXX
This removed all sets, including base. The individual packages are still there. I did not touch them.
If I now attempt to run "pkg autoremove" to see which packages need to be marked manually installed, pkg goes into infinite loop, gradually consuming memory at a rate of 1 MiB every 5 seconds.