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.


We can't merge these README changes into the main repo. You'd have to add the "feature I added" section inline with the rest of the jsdox documentation. 

@psq We should consider pulling documentation into the README of JSDox instead of relying on contributors to update the gh-pages branch. It's a more streamlined flow to just use the readme as the source of documentation. If you agree, then @vdeturckheim can add a new section to the readme called "Features" that looks kind of like:

```md
### CLI Options

`-recursive` (alias: `-r`): it does this and that...`

Example:
`jsdox -r path/to/my.js`

Produces the file `path/to/my.md`

`-respect-recursive` (alias: `-rr`)...
```