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.


I updated my IDE settings to be compliant with spacing rules.