Hi,
With the default configuration, dune cache clear leaves ~/.cache/dune/toolchains in place.
I understand the technical reason, but it's a bit confusing. I think that the goal of dune cache clear is to replace rm -r ~/.cache/dune but it's now necessary again.
If removing the toolchains cache by default is not desirable, maybe an extra flag to remove this cache would work.
(noting the caveat in #11584 that these might not be in the same location)