Updated to new yaml-cpp API.

The new API was introduced in version 0.5.0. Since it is very different
(and in my opinion very much better) than the old API, the upgrade in
this code was worth doing.
Migrating build system to Autotools.

CMake is certainly easier to use for simple projects - the "time to
science" is lower than that of Autotools. But eventually I realized that
CMake actually a huge pain to use because a.) the documentation is
*abysmal*, and b.) it uses an enormous number of "local" environment
variables under the covers and then cobbles them all together, which
makes managing, e.g., the include flags or compiler optimization
settings for certain files, nearly impossible. Autotools, on the other
hand, is challenging to learn, but immensely more powerful once you've
figured out how to use it.
Added a few more junk files created by Autotools to .gitignore.
Removed CMake files.

We're switching to Autotools so we don't need these anymore.
Replaced CMake dependency in README with Autotools.
More fixes to Autotools files.