Fixes of autotools files

These commits try to fix:
dist* targets, so that source packages can be recreated reliably;
out-of-tree compilation.

These commits also update some automatically generated files (swig, help2man and man2html), while they do not update autotools generated files.

I think that autotools generated files should be removed from the repository (I have not done this yet). Do you agree? If yes I will drop those files.