Silence autotools warning

Modern autotools complain that

warning: autoconf input should be named 'configure.ac', not
'configure.in'

The file is explicitly used in autogen.sh, which needs to be updated
consistently.
Cleanup autogen.sh

Remove dead code and do not warn about configure being run without
arguments if configure is not going to be run at all.

This also makes it more consistent with the mono autogen.sh.
Merge pull request #15 from ranma42/improve-autotools

Improve autotools