Use standard autotools doxygen support.

This uses ax_prog_doxygen.m4 which is part of the standard gnu
autoconf archive.  E.g.,

$ apt-get install autoconf-archive

This is invoked in configure.ac. It contains a snippet for inclusion
in Makefile.am, which is extracted and included via appropriate
machinations in autogen.sh and Makefile.am.

The doxygen target directory is moved to the default location.

Generation of PDF documentation is enabled by default, can be disabled
with

$ ./configure --disable-doxygen-pdf
Update git ignorance.

Git ignore doxygen debris.
Be more specific about our git ignorance.
Generally refresh the .gitignore list.