Squashed commit of the following:

commit 3b1952b9b9e485fa8d4c93705e95eb62376edc9f
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Feb 21 20:01:05 2013 -0500

    Write exact solution for collapse1d problem

commit 91aa9b5a026eb1839d709e446d9aff4647a61331
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Sun Feb 17 14:01:50 2013 -0500

    Give blobs problem a size parameter to zoom in on contact layer

commit 40b1777e38fd718f8e7710417679b8051f175309
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Sun Feb 17 00:02:38 2013 -0500

    Add a sequential HDF5 write option to the unigrid module

commit 60ed4c0a897922d808bc99cd17f24bfa3b0fce97
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Sat Feb 16 23:02:55 2013 -0500

    Set up a blobs problem (hijack KH for now)

commit 0f9d8ea7fb48e09b9419a2bd61c84bac90e9cbc8
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Tue Feb 19 12:23:28 2013 -0500

    Add physical BC flag to blocks

commit 63931c484c233e7d74572efe55ec5dcb0403c955
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Feb 18 20:03:40 2013 -0500

    Remove grav1d from the fish solver set alltogether

commit 78919ea98fd236c6ff44109aed94b84663b81cc7
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Feb 18 18:15:43 2013 -0500

    Add a FishScheme class and other things

commit 16f5aa4a994ec41f71a8ade13c9b065eeb0c962c
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Feb 18 17:04:35 2013 -0500

    Take small steps in Lua code toward letting blocks support gravity

commit 6bd7efdc6e286743f262b07f9b923a008db2c797
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Feb 18 17:03:48 2013 -0500

    Fix a crucial bug in array module: make a deep copy of input arg tables

commit f4bd4a87dc9278ca68f0c4ea70f01f4953b32c10
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Feb 18 16:39:56 2013 -0500

    Add the poisson.c file to fish, start to phase out grav1d.c

commit e3571d1e2bc7c45327c6e9236167fb8f59f01e54
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Feb 18 16:12:24 2013 -0500

    Do a few more style adjustments

commit 0d5c3bb509f2fc4d722f37808dc7edc2f1974eab
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Feb 18 13:30:56 2013 -0500

    Change up doc style a bit

commit 66999d72252259cdd10d959089f326b9acd57ac2
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Sun Feb 17 19:05:33 2013 -0500

    Fix a typo in the KH setup

commit 3fddaefd2f6d696f4483c3e429a0387e17d93655
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 23:32:00 2013 -0500

    Add the index.html page

commit 2050b672a693f27bb09e96028730fe11020988a9
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 23:32:00 2013 -0500

    Possibly publish a version of the Mara test page

commit 6c551571db7d06bd71f0835aed0f79e1d72a3ae4
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 22:52:19 2013 -0500

    Update docs with exact Riemann solver

commit eecf27bd2a49b590983b0cb438d1030019fe0447
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 18:47:18 2013 -0500

    Update the KH image in TestProblems.org: but WENO5 versions are outdated

commit 431f109ca21987cd9007e002a405be641ecad952
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 18:44:30 2013 -0500

    Add an h52png.lua tool

commit ad33eb4c4063af967a34b54869201f77316f0ff2
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 18:33:44 2013 -0500

    Add visual.write_ppm function

commit 7678a83787fb59535e7404b34bb2f130e1dbac1f
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 18:15:38 2013 -0500

    Try a KH setup which is easier to write down, images are still outdated

commit acb7d02e3519c87da0a2662d5804b1a8b81c789f
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 17:54:48 2013 -0500

    Fix a major (two-headed) bug having to do with Mara and MPI

    1. Mara/Makefile did not build mara.cpp with the DEFINES macro. This
       lead to the subgrids.hpp typedef'ing DecomposedCartesianDomain to
       SimpleCartesianDomain.

    2. The result of unigrid:local_mesh_size('shape') cannot be used as
       input to Mara's set_domain function: Mara expects the global domain
       shape as input.

commit 120ec6af0bc75ea70613d86b5f51892cc83b52c6
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 15:29:40 2013 -0500

    Update the tests-1d script

commit 266e0b210579578cbe25be4b08e9376d2db3e0c9
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Feb 15 14:09:16 2013 -0500

    Improve the class module MRO: breadth-first search

commit 4def508de3d3f8bd632b7b417b76f03f97dc0c9d
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Feb 14 22:53:51 2013 -0500

    Contintue doc and testing

commit ed17544b8a0ceda6f049d23c1c903d0d1d691a72
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Feb 14 12:55:54 2013 -0500

    Add a description of the KH problem to doc

commit 298ab48f305c3660bd2cca25b728e5f494820e75
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Feb 14 11:04:00 2013 -0500

    Continue writing and documenting test problems

commit a61adf37e07fbbbdb778e776f87e8ba6090a2524
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Feb 13 21:07:06 2013 -0500

    Start documenting shock-tube problems

commit d558d741dda8566f54745e00f6b0ae1d9836d8f3
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Feb 13 20:06:39 2013 -0500

    Write the SoundWave problem description and convergence test

commit 9dd02251aa3b7dcb79cbef74c985bed3b1ce1d70
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Feb 13 18:40:08 2013 -0500

    Add a bunch of documentation data and markup, get ready for thesis work