title: yuidoc parses but no output and no errors
body: <p>I've spent the last 4 days trying to get yuidoc to parse my javascript framework and it's really starting to drive me nuts.</p>
  
  <p>here is my json config file</p>
  
  <pre><code>{ linkNatives: 'true',
    attributesEmit: 'true',
    paths: [ '..\\\\layers' ],
    outdir: '../docs/',
    port: 3000,
    nocode: true,
    extension: '.js',
    project:
     { name: '{NAME}',
       description: '{DESCRIPTION}',
       version: '1.0.0',
       url: 'http://docs.mysite.com/',
       logo: 'http://docs.mysite.com/img/logo.png',
       themedir: 'yuidoc-bootstrap-theme' } }
  </code></pre>
  
  <p>It is parsing the json config and there are no errors. Here is the output:</p>
  
  <pre><code>$ yuidoc ../layers
  info: (yuidoc): Starting YUIDoc@0.3.46 using YUI@3.9.1 with NodeJS@0.10.24
  info: (yuidoc): Scanning for yuidoc.json file.
  info: (yuidoc): Loading yuidoc.json data from:    C:\devtools\GitHub\Framework\tools\yuidoc.json
  info: (yuidoc): Starting YUIDoc with the following options:
  info: (yuidoc):
  { linkNatives: 'true',
    attributesEmit: 'true',
    paths: [ '..\\\\layers' ],
    outdir: '../docs',
    port: 3000,
    nocode: false,
    project:
     { name: '{NAME}',
       description: '{DESCRIPTION}',
       version: '1.0.0',
       url: 'http://docs.mysite.com/',
       logo: 'http://docs.mysite.com/img/logo.png',
       themedir: 'yuidoc-bootstrap-theme' } }
  info: (yuidoc): YUIDoc Starting from: ..\\layers
  Nlaak@Nlaak-PC /cygdrive/c/devtools/GitHub/Framework/tools
  $
  </code></pre>
  
  <p>I can get it to work using command line and default settings for output and theme but it does not have my project build and version info. The Bootstrap theme is on Github and does work. I am using Cygwin 64 Bit on windows 7 64 bit.</p>
  
  <p>I have...
  - Checked line endings
  - Copy and pasted yuidocs examples with minimum editing
  - tried command line every which way
  - verified all paths and directories exist</p>
  
  <p>HELP! Why is there no errors and no output.</p>