[cctbxbb] Sphinx docs for CCTBX

[Nathaniel Echols]

Thanks to some superb work by Nader Morshed, Oliver Zeldin, and Ian Rees,
we now have automatically updated Sphinx docs for CCTBX:

http://cci.lbl.gov/cctbx_docs/

Obviously these are still pretty sparse - right now most of the formal
documentation is clustered here:

libtbx
libtbx.utils
libtbx.phil (mostly re-using Ralf's old documentation)
cctbx.miller
iotbx.pdb (built on Ralf's newsletter article)
mmtbx.command_line

These are a combination of inline docstrings and separate restructured text
files in cctbx_project/sphinx.  We have automatically generated rst files
for some modules, but others will need to be added manually.  In the end I
think we'll want to curate every file, but the current layout will get us
started.  To facilitate additional contributions, I've modifed the
installation script for base packages to include a --sphinx option.  After
setting up CCTBX you can then do this:

cd $BUILD
libtbx.configure sphinx
cd $SRC/cctbx_project/sphinx
make html

and you will get the full documentation built locally.  I am still figuring
out how to use Sphinx effectively; it is definitely possible to document
Boost.Python extensions but it's not quite as obvious.

I don't expect us to retroactively document several hundred thousand lines
of code written over a decade, but if we can get the core parts thoroughly
covered that will greatly reduce the barrier for new developers.
 Suggestions for particular modules to focus on are appreciated; I am going
to try to cover the basic PDB+reflection file functionality.  I encourage
anyone doing CCTBX-related development to contribute as you go.  (They
don't need to be your own APIs, just modules you're reasonably familiar
with.)  Those of you who already have a ton of undocumented code can expect
me to harass you periodically about fixing this.

(Note that I've cannibalized at least one newsletter article for this, and
continue to do so; we should re-use existing prose descriptions as much as
possible without violating copyrights.)

-Nat
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