Enabling Markdown and other JSDoc improvements

This change enables GitHub flavored markdown for APIdoc
comments. The code example in map.js shows how to use markdown
for code snippets. doc/index.md is now included again as start
page for the docs. Everything in the doc/tutorials directory
will also be added to the docs as tutorial. As an example, I
moved the ol3.md file with the architecture to the tutorials
directory.

Currently properties and methods annotated with @inheritDoc
or @override won't be documented at all. This is a known issue,
so I added a custom JSDoc plugin with a hack to avoid this.