This commit updates make_deps.sh to build newer versions of Blitz (1.0)
and fftw (3.3.9).  The 2010 version of Blitz no longer builds with the
newest versions of GCC, and there is no harm in updating FFTW.

The newest versions of Blitz (github head) require cmake to
build, and some systems still in use have old, incompatible versions of
cmake.  Blitz 1.0.2 requires python to complete its build process (some
files are auto-generated).

The new version of Blitz dropped the blitz::Vector type, being
equivalent to a 1-dimensional array, so it was replaced with
blitz::Array<type,1> instead.

Additionally, the Parformer (parallel transpose) code was adjusted to no
longer use MPI_UB to define the upper bound of the array section
datatype.  MPI_UB was deprecated in the MPI-2 standard and removed in
the MPI-3 standard, so SPINS could fail to build with some new MPI
libraries (OpenMPI 4.0.3 is confirmed to break).

Because this commit updates dependencies, the patch version is
incremented.

Some fprintf statements were written as stderr and should be stdout

- Added 1D and 2D outputs
- Added parallel writing and reading

The matlab readers incorrectly interpreted 58 as ':', which resulted it in returning a vector rather than a scalar when index 58 is requested.

As compiler versions march on, some previously-valid code was generating
warnings; these have been corrected.

*) In Plan_holder and T_util, using <ext/hash_map> was generating a
deprecation warning.  The proper replacement for the GCC <hash_map> is
the STL <unordered_map>, however that is part of the C++-0x standard
that is not yet supported by default in GCC 4.3-4.6, requiring a
compile-time command-line flag.

Since implementing *that* over a broad range of systems will be
extremely difficult, the better option for now is to silence the
deprecation warning by selectively undefining __DEPRECATED around the
inclusion of <ext/hash_map>.  This preserves any GCC deprecation
warnings around other bits of code.

*) In T_util and gmres_1d_solver, "literal string constants" were being
assigned to char *, when string literals are supposed to be const char
*.  This reflected an error in the variable spec; there's no reason that
the assigned-to-vars couldn't themselves be const char *.

As of this commit, the code compiles (make cases/bench_dipole.x)
compiles warning-free on belize.

This is the initial commit of SPINS to a git repository, coming from
an essentially unmanaged environment.  While this is a *complete*
archive, this is probably not the most useful form for development
going forward.  Notably, the future management should be:

1) Pare down the case files

2) Establish branches for individual users.  Not as a long-term goal,
   but instead to keep user-specific case files from lingering in
   the main repository long after their use is obsolete.

2b) Establish semipermanent branches for typical users.  A release
   branch should include the basic documentation cases, a benchmark
   case should include benchmarking cases, and there are probably
   others that aren't coming to mind now.

3) Add helpful MATLAB processing scripts to the repository.  Too
   much of that is ad-hoc now, completely unmanaged.

4) For papers/etc, establish tagged versions.