One thing I noticed after a bit further investigation (and if I didn't misunderstand), it looks like it may not be possible to compile Clojure without a copy of previously compiled spec.alpha class files. The spec.alpha .clj files are not sufficient. I imagine that may well be intentional, but thought I'd mention it in case not, or in case I did misunderstand.
I noticed because I thought Debian might be able to keep Clojure by shifting .clj compilation to install time. That did work fine for Clojure itself and Leiningen, two of the main cases where it would matter, but it looks like it won't work for clojure and spec.alpha if the conclusion above is correct.
Since clojure and spec.alpha appear to work when neither of them are compiled, Debian may be able to proceed that way, with of course much slower clojure, lein, etc. startup.
I'd thought maybe the clojure namespaces (from build.xml) could at least be compiled, but that provokes a crash if spec alpha isn't compiled. [edited after realizing that having both uncompiled does work]