Support `dune clean` over RPC

[shonfeder]

Expected Behavior

dune clean works when a watch server is running

Actual Behavior

$ dune clean
Error: A running dune (pid: 3600618) instance has locked the build directory.
If this is not the case, please delete "_build/.lock".
↳[1]

[shonfeder]

A alternate approach is to deprecate/remove dune clean entirely (see #12976), or print a dedicated message explaining why/that this command is incompatible with dune watch.