Squashed commit of the following:

commit bdd9a0d4024dde068d109158c9b326565e7c08c9
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Mar 31 10:41:11 2014 -0700

    Remove junk files

commit 5125104cfdfe5ff84d2461df5c96718caced09d7
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Mar 31 10:36:55 2014 -0700

    Complete updated build system

commit cce213d1cb671dcbf107d63b38ce44559bb50482
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Mar 28 22:22:37 2014 -0700

    Move source around and refactor build

commit 2c2886790861b9317ce15929ee0f314788986cc7
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Mar 28 18:28:58 2014 -0700

    Fix several things and partially put jet problem in Lua

commit f1d16cbd970d4dc0148842c25a028361a7485504
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 27 16:32:53 2014 -0700

    Put back limited support for the visualization code

commit c6b8e0a736b37e0d8e9960ca48c93af496056659
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Mar 26 22:14:36 2014 -0700

    Support model parameters in test problem class

commit 0049a6afcfb14d4995dc19c0d65f9206a0d342a0
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Mar 26 19:08:03 2014 -0700

    Add 3d EMF calculation, but not tested yet

commit 30d68fb82c027fe134dea933d2cceb9871b5d665
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Mar 26 18:13:08 2014 -0700

    Add HLLC riemann solver for nrmhd, move source to riemann.c

commit 002d592d45c50cb43698e90dbd893630a6f4efca
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Mar 26 14:26:40 2014 -0700

    Add HLLC riemann solver for nrhyd equations

commit 5f1b369523010dce4d10c9ff9e30a868bd3f8098
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Tue Mar 25 19:30:21 2014 -0700

    Fix last bug in nrhyd equations

commit 374a9dcd4e9c00908de7d298e299ca1924aac9d0
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Tue Mar 25 17:23:06 2014 -0700

    Work on finding bug in newtonian MHD

commit 2c990e9d7efeb95b5238938c437a7b9ba5f7ec24
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Tue Mar 25 10:37:42 2014 -0700

    Identify and fix several bugs, hard-code for 1d evolution

commit a8850851f3fd2be239988cdb1ea7c4ea94752325
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Mar 24 22:47:53 2014 -0700

    Fix a bug in the srhyd and srmhd equations, wrong tau expression

commit 6592659e78ced2c2252b3f934a7a15dfd710da0d
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Mar 24 18:20:16 2014 -0700

    Fix a bug with initial data on faces and edges, start testing problems

commit 7af4b39866380c4c8853341ad4683a1613a2ea47
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Mar 24 14:45:48 2014 -0700

    Write fast hdf5, refactor Lua code for m2

commit b7bbb128527728c890414d62e1691633807cc36a
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Mar 21 21:20:31 2014 -0700

    Fix bugs and get flux BC's working from Lua

commit 44a7656cf632536e4244e197f3d0da0e3853e130
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Mar 21 17:13:48 2014 -0700

    Improve m2 wrap and struct interface together

commit aa75c9ac51b5c0951ecd2de5f7e2df89b26452a3
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Mar 21 12:36:26 2014 -0700

    Finish all boundary conditions callbacks

commit 2df8c5eed9920cecd7220b5e227f018c308f62c6
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 20 22:20:08 2014 -0700

    Add prim and aux data structures

commit 74387718737fe59851dc6f0037a06f8ed94752c1
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 20 18:46:05 2014 -0700

    Put in initial conditions function callbacks

commit 716f4adbfaca94bd3830619cbafe375353867926
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 20 16:48:58 2014 -0700

    Write a volumes iterator

commit d7242499a0af1be50c4a967ac53395d2048d46b0
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 20 12:31:45 2014 -0700

    Get good reference management system working for structs

commit 00561440bdd05212835fe4edff5a498f36a32915
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 20 09:31:34 2014 -0700

    Change struct scheme so that the userdata is just a pointer

commit 09b5024727e96d9f8efbe66a418759fbc1a942bd
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Wed Mar 19 19:27:26 2014 -0700

    Improve how struct works

commit 2119fd471b42a8ded3a7ac1ff923d0c48b80588b
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Mon Mar 17 13:47:55 2014 -0700

    Evolve zulu a bit

commit 2016f862ee484058952e2ded706a00f9247733ed
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Mar 14 16:01:54 2014 -0700

    Allow sub-structs in Lua struct description

commit aad70177e2d79640101ab17416c23a0c807404a1
Merge: dac471a 84355e8
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Fri Mar 14 10:22:56 2014 -0700

    Add 'src/zulu/' from commit '84355e85099a7f4b869eba55fc3a862c89bca6f5'

    git-subtree-dir: src/zulu
    git-subtree-mainline: dac471a65a819eee9682eb7214fe5f22e2b0ec5e
    git-subtree-split: 84355e85099a7f4b869eba55fc3a862c89bca6f5

commit 84355e85099a7f4b869eba55fc3a862c89bca6f5
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 13 21:16:13 2014 -0700

    Add code for first zulu commit

commit dac471a65a819eee9682eb7214fe5f22e2b0ec5e
Author: Jonathan Zrake <jonathan.zrake@gmail.com>
Date:   Thu Mar 13 21:51:34 2014 -0700

    Add a m2vol_neighbor function which was handy for flux BC's
Update Makefile.in.template