One more strange fact: When you remove third-party, but run with the
released closure-library, you don't see the warning, but repl still doesn't
work. Thinking of it, I have run into that before.

So my theory is, that the build with the plain goog.jar fails because its
deps.js refers to ../third_party entries. This causes the build to fail,
even if a third-party jar is available on the classpath.
In http://dev.clojure.org/jira/browse/CLJS-276 this got fixed for the
release jars. Now that the repl depends on third-party too, it becomes
apparent that the goog.jar generated in bootstrap suffers from this issure
too.

So why are there no warings when compiling with just the official
closure-library?
The ../third_party entries get removed from the released jar here:
https://github.com/clojure/clojurescript/blob/master/script/closure-library-release/make-closure-library-jars.sh#L49
Supposing that, with an incomplete deps.js, closure compiler doesn't warn,
that would explain it.

I think this could be solved by regenerating a combined deps.js for
closure_library and third_party and unifying the build of the release jars
and the dev jars.

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