In the Meta-CVS project, I carried a copy of asdf.lisp in which the package was renamed to zxcv, to isolate from the ASDF churn and be able to run my version of ASDF possibly with my fixes even in a Lisp that has ASDF preloaded.
ASDF is the only build system I know which broke on me when I tried to fool it with a link farm (lndir command) into building in a separate directory. It resolved the paths using the truename function which eliminates symbolic links, and then calculated the .fas file names from the canonicalized paths, thereby depositing compiled files into the original directory rather than in the symbolically linked tree.
ASDF also depends on symlinks for external organization. .asf files are often symlinks to the real location, and without these symlinks, things don't work.