Fix incompatibility with Twig v1.33.2

Instantiation of Twig_Loader_Filesystem was failing on second parameter, which is expected to be a string variable representing file path common to path passed in first parameter, not a setting array as is passed in current version of this class in master.  I did not check impact on other areas of code (i.e. impact of removing cache/debug settings), but simply removing this parameter allow markdown generation to work in my environment.

Closes #13

Upgrade twig

Adding way to change what the api index markdown file is called and updating readme to reflect change.

Use dirname(__DIR__) instead of '__DIR__./../templates' in phpdocmd bin, no need to use file_get_contents when using 'Twig_Loader_Filesystem' class as loader.

Upgrading twig/twig to '~1.2|2.0' in composer.json, using 'Twig_Loader_Filesystem' for loader and using 'Twig_SimpleFilter' for adding 'classLink' twig filter.

Clean up

Fixes #7.

Switching to array_merge fixed this.

Added installation instructions

Generator: class-linking.

The links should point to the .md file itself. Without the .md extension
you'll get a 404.