We've gotten a couple of bug reports from users who are having trouble doing (ccl:rebuild-ccl :clean t) when (require 'asdf) is in their init files.
http://trac.clozure.com/ccl/ticket/765 http://trac.clozure.com/ccl/ticket/773
While it's undoubtedly best to start up without an init file when you're planning to rebuild the lisp (by using "ccl -n"), I'm wondering if there would be some way to avoid this particular issue involving ASDF.
During the process of rebuilding ccl, we compile (but do not load) ccl:tools;asdf.lisp. Perhaps we could simply stop compiling ASDF as part of ccl:rebuild-ccl. That way, the compile-time side effects that seem to be causing the trouble would be avoided.