Rework options parsing to use grunt's built-in options parsing and fix `outDir` location.

I found it frustrating that this module would not respect this common type of configuration used in grunt >= 0.4.0:

```javascript
docker: {
  options: {
    // Common options for all tasks
    lineNums: true
  },
  ui: {
    src: ['ui/**/*.js', 'ui/README.md'],
    dest: 'docs'
  },
  node: {
    src: ['nodejs/lib/**/*.js', 'nodejs/README.md'],
    dest: 'docs'
  }
},
```

This PR enables the use of `this.options()`, provided by the task interface in Grunt.

There was a bug related to input directories; code inside Docker does some pretty bad munging of `options.inDir` and `options.outDir`, and as a result we need to fiddle with the `inDir` property if the documentation is being generated from a directory above this one.

I've also added a few bugfixes, removed some dead code, and added some notes related to the input/output directory.