renames files for autoconf

With autoconf, we can no longer compile .c files using CXX. They
have to have the ending .cpp or an error will be thrown. Also the
Makefile is now generated by automake.
switches from manual make files to automake
adds GNU style files
adds configure script
adds configure.ac script
improves .gitignore to ignore various autoconf files
Merge branch 'master' into autoconf

Conflicts:
	src/Makefile
generate a README from README.md to satisfy autoconf
fixes readme to reflect autoconf changes
adds missing file
cleans up makefiles
prepares for better documentation
Merge branch 'master' into autoconf
adds rough man page
adds various files to build process
changes version number to conform to debian standards
Merge branch 'master' into autoconf
removes missing file
improves readme
adds missing to gitignore