[...]
Davy> These files are listed in the DIST_COMMON (at least I'm pretty sure
Davy> DIST_COMMON is where these files are coming from in the cp commands)
Davy> so I'm not explicitly listing them myself anywhere to be distributed.
Davy> I've tried several versions between and including 1.6.3 to 1.7.5
I think you should definitely revise the way you use EXTRA_DIST
in your Makefile.am. Automake is designed to distribute files
using an opt-in strategy. Most of the times, Automake can
figure automatically what files to distribute. Sometimes, there
are a few files that Automake does not know about but that you
want to distribute: you should list each of these files in
EXTRA_DIST.
What your Makefile.am tries to implement is an opt-out strategy:
all directories are listed in EXTRA_DIST, and with a dist-hook
you clean the mess by removing most of the unwanted cruft. This
will only get you into trouble.
EXTRA_DISTing directories should be reserved to directories with
generated/dynamic contents. Perhaps they can be useful in other
situations too, but at least EXTRA_DISTing a directory which
appears in SUBDIRS looks really awkward (your config/ directory
is not in SUBDIRS but you have a few other directories in this
situation).
The (more specific) error you report is related to the fact that
Automake has already decided to distribute the files from
config/ that it needs (those you mention), and yet you are
EXTRA_DISTing this config/ directory. Some implementation
details prevent a file from being distributed both individually
and as a directory member.
For more on this config/ issue, see PR/390 in the Automake Gnats
database. A related topic to EXTRA_DISTing subdirectories is
the use of wildcards: there is a entry about this in the
Automake FAQ (in recent manuals).