Pyvoro

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* Carried out a major overhaul of the source code comments that are used by
Doxygen. Several errors in the documentation were fixed.
* Additional comments in the Makefiles, and added the "phony target" keyword
* Many code cleanups and standardizations. Some double and triple loops
were concatenated into one to reduce the amount of indentation.
* Fixed the import.cc example program
* Updated Doxyfile to version 1.6.1

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* In response to feedback from several people, the routines for computing
statistics about computed Voronoi cells have been significantly revised,
extended, and put within a common framework. The voronoicell class now has a
large number of routines of the form output_...() that will print cell
information to an output stream. There are also a number of new, simple
routines for computing basic statistics such as the number of edges and faces
of each cell. All of these routines can now be used during the container
analysis, by making use of the new print_custom() routine, which can output
according to a given format string, that uses control sequences similar to
the standard C printf() routine.
* Renamed the "radical" example directory to "custom", and added two
new programs called "cell_statistics.cc" and "custom_output.cc" for
demonstrating the new output routines for the voronoicell and container
classes respectively
* Added a routine for computing the centroid of a Voronoi cell
* Added new routines for computing neighbor normals, in response to a
request from Dave Greenwood
* Removed unnecessary trailing tabs and spaces in the source code
* Fixed a few text justification problems, and altered some of the comments
in the example programs
* Improved the command-line utility, allowing it to specify custom information
in the output. Implemented better error checking on command-line arguments.
* Removed the facets() routine, since this has been superseded by the new
output_...() routines. This also rendered some functions in the neighbor_none
and neighbor_track classes obsolete, and they have also been removed.
* Some reorganization of the cell.hh and container.hh header files to group
similar functions together
* Added torus.cc example that shows how to write custom walls as derived
classes
* Updated Doxyfile to version 1.5.9

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* Added some missing cstdlib and cstring header files that cause compilation
errors on some systems
* Some text cleanups in the main README file and cmd_line.cc
* The worklist_gen.pl script was in DOS format. It has been switched to Unix
format to match the rest of the code.
* Fixed some incorrect inequalities in degenerate2.cc
* Improved some error messages in container.cc

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* Significantly improved the error messages generated by the code. It now
makes use of the exit() routine rather than throwing errors, and it returns
various status codes (defined in config.hh) for different types of abnormal
behavior.
* Changed two occurences of "cin" to "cout" in the draw_particles routines
* Corrected error in comment in the tetrahedron example
* Minor comment cleanups of the worklist_gen.pl script
* Updated Doxyfile to version 1.5.8
* Added a routine print_facet_information() in response to a problem
from Hengxing Lan
* Many of the cell based statistics routines (like number_of_faces() and
facets()) internally track their progress by temporarily flipping the edge
table entries to negative values, so that they know where they have already
been. The common code that was used at the end of each of these functions for
resetting the edges back to positive has now been made into a private inline
function called reset_edges().
* Fixed a missing initialization of max_radius to zero in the radius_poly
class. This should not have ever caused any errors, as max_radius would
always have been big enough. However if max_radius was initially set to a
large value, it could have potentially made the code run slower.
* Fixed the code layout in the suretest class header
* Added some additional checks in the command-line utility to screen out
invalid command-line arguments. Switched the test on the number of
computational blocks to use floating point arithmetic, because integers
could potentially overflow and become negative.
* Included several more of the POV-Ray header files that were used to create
the example images on the website
* Removed a "cout" statement in the wall_cone class
* Cleanup of the README files for the basic examples and the wall examples

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* Added the DOE acknowledgements to the code overview document

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* Added the code overview PDF document to the package, in the docs directory
* Fixed some spelling errors in the comments
* Many more documentation updates