Looks good, I have 3 more that I got rid of in @ivanov:matplotlib/minor_doc_fixes (I opened a pull request on your branch, Michael)

1.

/scratch/matplotlib/doc/sphinxext/inheritance_diagram.py:312: DeprecationWarning: xfileref_role is deprecated, use XRefRole
  'class', ':class:`%s`' % name, name, 0, state)

2.

/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:322: PlotWarning: Exception running plot /scratch/matplotlib/doc/mpl_examples/pylab_examples/loadrec.py
Traceback (most recent call last):
  File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", line 319, in render_figures
    run_code(plot_path, function_name, plot_code, context=context)
  File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", line 230, in run_code
    "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
  File "loadrec.py", line 17, in 
  File "/home/pi/tmp/local/lib/python2.6/site-packages/mpl_toolkits/exceltools.py", line 25, in 
    import xlwt as excel
ImportError: No module named xlwt

3.

/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:322: PlotWarning: Exception running plot pyplots/plotmap.py
Traceback (most recent call last):
  File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", line 319, in render_figures
      run_code(plot_path, function_name, plot_code, context=context)
    File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", line 230, in run_code
      "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
    File "plotmap.py", line 1, in 
  ImportError: No module named basemap

Warnings which still remain:

Here are some warning that I did not get to the bottom of after a quick glance:

lots of WARNING: image file not readable for pylab_examples PDFs (I ran python make.py html --small)

/scratch/matplotlib/doc/mpl_examples/units/basic_units.py:119: DeprecationWarning: object.__new__() takes no parameters
  return object.__new__(cls, value, unit)
/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py:322: PlotWarning: Exception running plot /scratch/matplotlib/doc/mpl_examples/units/artist_tests.py
Traceback (most recent call last):
  File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", line 319, in render_figures
    run_code(plot_path, function_name, plot_code, context=context)
  File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/sphinxext/plot_directive.py", line 230, in run_code
    "__plot__", fd, fname, ('py', 'r', imp.PY_SOURCE))
  File "artist_tests.py", line 30, in 
  File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/collections.py", line 852, in __init__
    self.set_segments(segments)
  File "/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/collections.py", line 861, in set_segments
    seg = np.asarray(seg, np.float_)
  File "/home/pi/tmp/local/lib/python2.6/site-packages/numpy/core/numeric.py", line 284, in asarray
    return array(a, dtype, copy=False, order=order)
ValueError: setting an array element with a sequence.

/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/pyplot.py:docstring of matplotlib.pyplot.hexbin:129: (WARNING/2) Inline interpreted text or phrase reference start-string without end-string.
/home/pi/tmp/local/lib/python2.6/site-packages/matplotlib/pyplot.py:docstring of matplotlib.pyplot.annotate:13: (ERROR/3) Unexpected indentation.

also, not sure if this matters, but I'll mention it anyway:

checking consistency... /scratch/matplotlib/doc/devel/gitwash/dot2_dot3.rst:: WARNING: document isn't included in any toctree
/scratch/matplotlib/doc/examples/index.rst:: WARNING: document isn't included in any toctree
/scratch/matplotlib/doc/faq/environment_variables_faq.rst:: WARNING: document isn't included in any toctree
/scratch/matplotlib/doc/mpl_toolkits/axes_grid/index.rst:: WARNING: document isn't included in any toctree
/scratch/matplotlib/doc/mpl_toolkits/mplot3d/index.rst:: WARNING: document isn't included in any toctree
/scratch/matplotlib/doc/users/arraydata.rst:: WARNING: document isn't included in any toctree
/scratch/matplotlib/doc/users/plotting.rst:: WARNING: document isn't included in any toctree

I'm not sure how to remove the "image file not readable" warnings. They occur because the PDFs are used to generate LaTeX (and the doctree is generated in such a way that it can output either HTML or LaTeX), but we aren't generating them when "html --small" is passed. For HTML, this is just an annoyance -- however, if the user does "html --small" and then "latex", the latex will fail. So "html --small" is a bit of a dangerous hack, but I'm not sure of the best solution.

I'm stumped by the "basic_units" example. I'm stumped by units in general in matplotlib ;)

The hexbin and annotate docstring warnings also stump me: both the input and output appear fine, so I'm not sure what docutils is complaining about.

As for the orphaned rst files, I think I'll use "git blame" to follow up with the authors of those files to determine if they should be linked up or removed.