I realized just now that I haven't fully answered your question:
Michael Tautschnig wrote: [...]
how did you fix it
[...]
We had two problems interacting.
The first one was that distributed built docs were depending from non-distributed built files. This has been solved by following the guidelines in Section 27.5 of the Automake manual. The corresponding commit is the following:
http://www.cs.unipr.it/cgi-bin/cvsweb.cgi/ppl/doc/Makefile.am.diff?r1=1.92;r...
The second problem was that we were cleaning the distributed documentation. Why? Because otherwise we had a `make distcheck' failure. In this case we chose to follow what said in Section 14.4 of the Automake manual, adding (in the top-level Makefile.am):
distcleancheck_listfiles = \ find -type f -exec sh -c 'test -f $(srcdir)/{} || echo {}' ';'
[NOTE: the actual reason I am telling all of this is that I would like to know if there are better ways of solving the issue ...]
Cheers, Enea.