ENH: Update pre-commit hooks.
COMP:  Install ITKv4 and VTK to reduce include paths.

When pointing ITK_DIR or VTK_DIR to a build tree, the include paths
are very long.  By installing these packages, the include paths become
significantly shorter.

This facilitates several development tools that need to search for includes
to work faster (including compilers themselves, but clangcomplete and cppcheck
in particular).
ENH: Update ITKv4 to include DCMTK clang build fixes.
ENH: Remove unused function identified by cppcheck.
COMP: cppcheck identified untested function.

style: The function 'itkResampleInPlaceImageFilterTest' is never used
ENH: Code cleanup by cppcheck for BRAINSMush
ENH: Improve copyright statement of BRAINSMush

This effort was supported by the ITK and NAMIC
software engineering projects, and should have
compatible licenses with those projects.
STYLE: BRAINSFitEZ syncronizaiton with BRAINSFit

BRAINSFitEZ and BRAINSFit should be as close as
possible in the actual source code, but the xml
presentations are different.
ENH: Localize variable to prefer initialization to assignment.
STYLE: Exception handeling issue identified by cppcheck

style: Throwing a copy of the caught exception instead of rethrowing the original exception.
BUG: Duplicate if expression due to copy-paste-bug

style: Found duplicate if expressions
PERF: cppcheck identified performance gain

performance: Function parameter '_arg' should be passed by reference.
PERF: Function parameter should be passed by reference.

for i in *.cxx *.hxx *.h ; do
   /usr/local/bin/cppcheck -q --enable=all --force --inline-suppr --includes-file=~/Desktop/IncludesBSA.list --template=gcc $i;
done > /tmp/cppcheck_warnings 2>&1
sort -u /tmp/cppcheck_warnings | sort -t: -k 4 > /tmp/orgainized_cppcheck_warnings.err

vim -q /tmp/orgainized_cppcheck_warnings.err

performance: Function parameter 'debugOutputDirectory' should be passed by reference.
COMP: Potentially uninitialized values

In error cases, or some paths of the logic it was possible
that variables were uninitialized.

error: Uninitialized variable: baselineImage
STYLE: cppcheck match signed types

warning: %u in format string (no. 1) requires an unsigned integer given in the argument list.
STYLE: operator= should return reference to self.

style: 'Brains2LandmarkReader::operator=' should return 'Brains2LandmarkReader &'.
STYLE: Make types match

warning: Comparison of a boolean with an integer
STYLE: cppcheck Consecutive return, break, continue, goto or throw statements

style: Consecutive return, break, continue, goto or throw statements are unnecessary.
ENH: Make loop index constant end.
STYLE: Exception should be caught by reference

style: Exception should be caught by reference.