=== Science ===
The directory Science/ now contains files corresponding to
the various functions in the now-removed Science.cpp.

Filenames correspond directly with the function name, and each
file contains only one functions, with a few notable exceptions.
 - Science/get_quads.cpp contains get_quads_x, get_quads_y, and get_quads_z
 - Science/compute_background_PE contains the helper function
compare_pairs

The global variables _quadw_x, _quadw_y, and _quadw_z are declared as
extern in Science.hpp and declared in Science/compute_quadweights.cpp

=== Makefile ===
The Makefile has been modified accordingly. It now automatically detects
all Science/*.cpp files and includes them in the compile recipe.

The Makefile has also been tidied up a little bit by defining a variable
SPINS_BASE which points to the core files.

In the previous merge, compilation of Sorter.o went missing from the
Makefile, and a typo was introduced in the gravity_current case file;
each would prevent a build from finishing.  These are fixed.

This changeset adds a compile-time option on whether to include the
timing code.  If SPINS is compiled without TIMINGS=true, the timing code
is #defined to a no-op and should not otherwise affect the performance
of the software; timing_stack_report will instead print a short error
message.

Because this affects #defines in header files, changing from
TIMINGS=true to false (or vice versa) should only be done with a 'make
clean'.  Not doing so could leave the timing code in an inconsistent
state and result in either link-time errors (if older code calls timing
code that is #defined away) or a corrupted/growing timing stack (if for
example a timing_push() is compiled in but the corresponding
timing_pop() is removed.)

This commit adds stack-structured timing code, such that bits of SPINS
can be instrumented with

>  timing_push("short name")
>  [... work goes here]
>  timing_pop()

This is recursive, such that already-timed portions of the code can call
the timing code to further instrument subroutines or discrete code
segments, and the resulting structure follows the -dynamic- call stack.
This does have the odd result that portions of the code that are re-used
(namely spectral derivatives) can show up as several 'leaf' nodes in the
graph.

To print out the report to standard error, call

>  timing_stack_report()

The exact format of the report should be considered tentative.

The pair of Transformer.[ch]pp files contained old code built for SPINS
before parallel transformation (over MPI) was fully implemented.  These
classes were replaced wholesale with Parformer.[ch]pp (Parallel
Transformer), but the older code remained in the repository.

Removing these files should not affect any active code.  It will affect
certain disued test cases (subject to changing #includes), but these
cases themselves need more serious maintenance to update for the
"gradient object" interface.

The case file source code is embedded into the binary at compile time.
At runtime, the source code is printed to spinscase.cpp. This eliminates
the need to maintain a copy of the case file alongside the binary.

This adds -lblas to the lapack library flag, because with the last
update the toolchain on Belize is more strict about implicit library
inclusions.

Also, the library flags have been re-ordered in the general makefile,
going (roughly) from most specific to least.

Also included an add_option speicalization for the string parameter
type.  It's convenient to allow for const char * as a default value for
these parameters, but that poses a problem for the templated add_option
function because of the lack of automatic conversion to const string.
By including a specialized overload of the template (with
implementation in Options.cpp), this problem is fixed.

This library uses boost::program_options, which provides a command-line
parser that also reads key=value - style configuration files.
Options.c/hpp provides a simplified interface for cases-code, which
should make option-definition more natural.

On systems using the MKL library, including the MKL (via $(LAPACK_LIB))
brings in the MKL fftw-wrapper bindings, rather than fftw itself.  This
is problematic on account of the fact that the MKL fftw wrapper doesn't
implement the parts of the library that SPINS actually uses; this leads
to an assertion failure on startup.

Also tweaked make_deps to properly install AMD and to
pick up on SYSTEM_CFLAGS (necessary for 32/64-bit
switch on plata).  Consequently, added SYSTEM_CXXFLAGS
since -Wno-deprecated is inappropriate for pure-C

The MPICXX flag is necessary because the blitz configure script
does not properly deal with the sharcnet 'compile' scripting
command; since it does not actually contain 'icc' in the *NAME*
of the command, the configure seems to default to a
blitz/gnu/bzconfig.h scheme -- which is then not found during
bona fide compilation.  This is probably an underlying bug in
the blitz build system.

bugs preventing make_deps from working properly with
library paths

in systems/ directory

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.