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

[ssafejava]

I found it frustrating that this module would not respect this common type of configuration used in grunt >= 0.4.0:

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.