title: sphinx-build fail - autodoc can't import/find module
body: <p>I'm trying to get started with Sphinx and seem to have relentless problems.</p>
  
  <p>Command: <code>docs/sphinx-quickstart</code></p>
  
  <p>I answer all the questions and everything works fine.</p>
  
  <p>Command: <code>docs/ls</code></p>
  
  <p>Everything looks normal. Result: <code>build  Makefile  source</code> </p>
  
  <p>Command: <code>sphinx-build -d build/doctrees source build/html</code></p>
  
  <p>It seems to work.  I was able to open the index.html file and see a "shell" of what I'm wanting.</p>
  
  <p>When I try and put my actual source code as the <code>source</code> folder I run into problems.</p>
  
  <p>Command: <code>sphinx-build -d build/doctrees ../ys_utils build/html</code></p>
  
  <p>Result:</p>
  
  <pre><code>Making output directory...
  Running Sphinx v1.1.3
  loading pickled environment... not yet created
  No builder selected, using default: html
  loading intersphinx inventory from http://docs.python.org/objects.inv...
  building [html]: targets for 1 source files that are out of date
  updating environment: 1 added, 0 changed, 0 removed
  Traceback (most recent call last):                                                                                               
    File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
      __import__(self.modname)
  ImportError: No module named ys_utils
  Traceback (most recent call last):
    File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
      __import__(self.modname)
  ImportError: No module named ys_utils.test_validate_ut
  Traceback (most recent call last):
    File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
      __import__(self.modname)
  ImportError: No module named ys_utils.git_utils
  Traceback (most recent call last):
    File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/ext/autodoc.py", line 321, in import_object
      __import__(self.modname)
  ImportError: No module named setup.setup
  
  /home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:4: WARNING: autodoc can't import/find module 'ys_utils', it reported error: "No module named ys_utils", please check your spelling and sys.path
  /home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:10: WARNING: autodoc can't import/find module 'ys_utils.test_validate_ut', it reported error: "No module named ys_utils.test_validate_ut", please check your spelling and sys.path
  /home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:12: WARNING: don't know which module to import for autodocumenting u'UnitTests' (try placing a "module" or "currentmodule" directive in the document, or giving an explicit module name)
  /home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:18: WARNING: autodoc can't import/find module 'ys_utils.git_utils', it reported error: "No module named ys_utils.git_utils", please check your spelling and sys.path
  /home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:24: WARNING: autodoc can't import/find module 'setup.setup', it reported error: "No module named setup.setup", please check your spelling and sys.path
  WARNING: master file /home/ricomoss/workspace/nextgen/ys_utils/index.rst not found
  looking for now-outdated files... none found
  pickling environment... done
  checking consistency... /home/ricomoss/workspace/nextgen/ys_utils/ys_utils.rst:: WARNING: document isn't included in any toctree
  done
  preparing documents... done
  writing output... [ 50%] index                                                                                                   
  Exception occurred:
    File "/usr/local/lib/python2.6/dist-packages/Sphinx-1.1.3-py2.6.egg/sphinx/environment.py", line 1213, in get_doctree
      f = open(doctree_filename, 'rb')
  IOError: [Errno 2] No such file or directory: '/home/ricomoss/workspace/nextgen/docs/build/doctrees/index.doctree'
  The full traceback has been saved in /tmp/sphinx-err-jjJ7gM.log, if you want to report the issue to the developers.
  Please also report this if it was a user error, so that a better error message can be provided next time.
  Either send bugs to the mailing list at &lt;http://groups.google.com/group/sphinx-dev/&gt;,
  or report them in the tracker at &lt;http://bitbucket.org/birkenfeld/sphinx/issues/&gt;. Thanks!
  </code></pre>
  
  <p>I am a complete newbie to Sphinx and relatively new to this kind of documentation.  Can anyone offer some suggestions?</p>
  
  <p>Edit:</p>
  
  <p>I'd like to be able to use a Makefile to handle this.  As of now I have two folders in my project.</p>
  
  <p><code>nextgen/ls</code></p>
  
  <p><code>docs ys_utils</code></p>
  
  <p>I need <code>nextgen/docs/Makefile</code> to generate the HTML for <code>ys_utils</code> and all other modules I'm going to have.</p>