*NOT READY* Refactor

Just an early PR to get a bird's eye view of the work in progress and establish some transparency.

Main efforts in this PR:

* Simplify key parts of the codebase to increase maintainability
* Isolate functionality into modules
* Deprecate the use of the `-rr` option and have `-r` absorb respecting the directory structure if the input is a directory
 * If the input is a file, then the markdown will be dumped into the root of the output directory (the old behavior of `-r`)
* Support the output being a markdown file: `jsdox myFile.js -o myOutput.md`

Fixes #49
Fixes #56
+1
On Sep 23, 2014 6:02 PM, "Pascal" <notifications@github.com> wrote:

> In .jscsrc:
>
> > @@ -68,5 +68,7 @@
> >    "requireDotNotation": true,
> >    "disallowYodaConditions": true,
> >    "disallowNewlineBeforeBlockStatements": true,
> > -  "validateLineBreaks": "LF"
> > +  "validateLineBreaks": "LF",
> > +  "requireSpaceAfterLineComment": true,
> > +  "safeContextKeyword": "self"
>
> bind won't help accessing the variables in the closures. If this ever
> becomes a problem, we'll remove, or add more names safeContextKeyword can
> take an array.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/sutoiku/jsdox/pull/72/files#r17942596>.
>