* I have created a domain specific for MATLAB called, "MATLABDomain" hosted 
in a fork of sphinx-contrib here:
https://bitbucket.org/bwanamarko/sphinx-contrib
* It is basically a copy of the pythonDomain with [pP]y converted to [mM]at 
and [pP]ython converted to matlab | MATLAB conserving case.
* added the setup function to add the domain as an extension at then end of 
matlab.py
    def setup(app):
        app.add_domain(MATLABDomain)
* I created it by running make-ext, then adding the domain module, 
matlab.py.
* I installed it using python setup.py install - no warnings
* I then added 'sphinxcontrib.matlab' to extensions and made the primary 
domain matlab
extensions = ['sphinx.ext.pngmath', 'sphinx.ext.mathjax', 
'sphinxcontrib.matlab']
primary_domain = 'mat'
* I use domains as usual, .. module: is a module
* It works perfectly, except for one thing, when I make html, the 
:ref:`modindex` on the index.rst page still links to
... /_build/html/py-modindex.html instead of ... 
/_build/html/mat-modindex.html
* in fact if I use that ref anywhere it always points to py-modindex.html, 
which isn't created
* mat-modindex.html actually is created and interestingly the "modules" 
link in the upper right hand corner in between "next" and "index" works 
fine, and links to the correct page.
... /_build/html/mat-modindex.html
* now for another twist, if I build latexpdf (using MikTeX), the link on 
the index page, :ref:`modindex` actually does work, and links to the MATLAB 
module index - weird.

* I have tried to debug exactly when the href to py-modindex actually gets 
written, but it is like looking for a needle in a haystack!

<li><a class="reference internal" 
href="py-modindex.html<file:///C:/Users/mmikofski/Documents/MATLAB/PVLifeDoc/_build/html/py-modindex.html>
"><em>Module Index</em></a></li>

Can anyone who has worked extensively with html writers and builders give 
me a clue to what is going on?

Jinja2==2.6
Pygments==1.5
Sphinx==1.1.3
distribute==0.6.36
docutils==0.10
sphinxcontrib-matlabdomain==0.1dev-20130425
Python 2.7.3 x64
Windows 7 x64
ReportLab
MikTeX-2.9

Thanks
Mark

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