Updating the .gitignore file to handle the automake and configure.
Pulling in changes from the ap1.1 branch to include JSON in the build.
Adding in notes and stub files to sketch out the planned format code.

- The README.markdown gives an overview of the entire codebase to hopefully allow others to grok the code faster.
- Started putting in Doxygen-based comments for new structures for documentation.
	- Using the /// commenting style instead of /** */
- Added the format headers and code files.