With regards to the autonaming exception stuff:
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There is a wishlist item #89826 ("-d autonaming exception") outstanding
on Bison. This wishlist item requests that Bison be changed to conform
to the documentation.

This bug is still open, and no entry stating that this change has been
performed is to be found anywhere in changelog.Debian.gz.

Changing this behavior, even though it brings it somewhat closer to the
docs, breaks existing code. A good amount of existing code, at that:
Suddenly, all code that used to include "parser.c.h" breaks.

While in the long run this change is probably a good idea --- naming it
"parser.h" does indeed make more sense --- suddenly changing the
behavior in woody so close to release is probably a bad idea.

Please revert this change, possibly giving an option to enable the new
behavior. Or, at the very least, document it promenently.

FYI: Bison now names output as follows:
parser.c=> parser.h
parser.cpp=> parser.hpp
parser.*=> parser.output

[ BTW: I doubt this is your fault... I'm betting FSF decided to change
  this on you and it slipped by. ]

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