Documentation Index and subdirectories parsing

* Generates an index 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.

Should be Travis test compliant!