Documentation Index and subdirectories parsing

* Generates an index (with the -i option) for the documentation of functions and classes with links to detailed documentation and source file. 
* The index is sorted alphabetically.
* -r option makes jsdox parse the subfolders of the directory given as argument and generates all documentation in the output folder.
* --rr option makes jsdox parse the subfolders of the directory given as argument and generates all documentation in subfolders with the parsed subfolders name. Those are created in the output folder.


Do you want me to fix this and prepare a new pull request ?

I plan also to take a look at the [line number issue](https://github.com/sutoiku/jsdox/issues/37) in a short future (depending on my uni obligation)