E3-1243: Enforce strict conditions on module existence

Originally we simply warned if `FOO_DEP_VERSION` did not refer to a real
module; this was necessary as some modules had legacy (non-e3) dependencies
defined this way. However, this has the unfortunate side-effect that missing
_modules_ would "pass" the build, with a failure only happening if some
version of the module existed (but not the correct one).