BUG: improper string to char * assignment.

std::string path=(/tmp);
const char * charpath = path.c_str();  // NOTE: VERY DANGEROUS!
path=/var/tmp;                         // NOTE: charpath is now invalid!

This was causing all _Compare tests to fail.  After this adjustment, all
tests are passing.
ENH: Remove old CMakeLists-old.txt file.
ENH: Organize tree with common code directory

Common code in various directories were not
being consistently maintained.  Slight divergence
had bug fixes/enhancements in only a few of the
replicated code bases.
STYLE: Force consistent formatting

The vtkReader.cxx vtkReader.h files are in 3 different locations
in the ukftractography dirctory.  All locations need to be fixed
but the formatting of each file is inconsistent.  By
applying a fixed consistent formatting (ITK style) it is easier
to ensure that the files are truely consistent and redundancies can
be removed.

This step will ease the comparision to code that can be moved into
the common static library directory.
COMP: All building for superbuild other than Slicer

When building ukf from within BRAINS, some paths were missing.
STYLE: Refactor common code in UKFCommonLib

Redundant naming of files and classes within same
named files did not have the same code.  This caused
many difficulties in understanding what the code was
doing, and it required redundant fixes to the code
when a problem was found.

After refactoring, all tests continue to pass so
it is assumed that the refactoring steps so far
are working properly.
COMP: All building for superbuild other than Slicer

When building ukf from within BRAINS, some paths were missing.
PERF: Forcing const correctness and using references rather than copies

Some profiling indicated that 17% of time of a critical path function was
being spent unnecessarily copying matricies that should have been const
and therefore a reference into the original was sufficient.
STYLE: Remove compiler warnings

unnecessary const on return warning
shadow variable warning
PERF:  Refactor LU for speed, needs testing.