These files are not lost, they are never built on architectures that do not support compilation of ocaml to native code. This seems to be a bug in the upstream Makefile:
OBJECTCMXA=$(OBJECTCMA:.cma=.cmxa)
install-library:
[...]
cp $(OBJECTCMA) $(OBJECTCMXA) $(FULLCOQLIB)
This should accomodate for the fact that there may be no .cmxa files.
-Ralf.
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