COMP: Move ITK find_package calls into each sub-project.

This commit simplifies how ITK components are associated with each
sub-project. Instead of maintaing a complex logic in 'BRAINSTools.cmake",
the list of component for each sub-project is generated using the
"WhatModulesITK.py" script.

To automatically prepend the find_package call to every sub-project and
reduce the amount of manual editing required, assuming the source of
ITKv4 are in /path/to/src/ITKv4, the following one-liner
has been used:

cd /path/to/src/BRAINSTools

for proj in `ls -d */CMakeLists.txt`; do \
  d=$(dirname $proj);
  echo Updating [$proj];
  components=$(../ITKv4/Utilities/Maintenance/WhatModulesITK.py \
    ../ITKv4 \
    $(find $d -type f));
  printf "#\n# ITK\n#\n${components}\n\n"|cat - $proj > /tmp/out && mv /tmp/out $proj;
done
COMP: Remove unneeded call to "cmake_policy"

Since calling 'cmake_minimum_required' with version X.Y.Z implies that
policy associated with version X.Y.Z will be set, this commit
removes the redundant call to "cmake_policy".

For more details, see [1]

[1] http://www.cmake.org/cmake/help/v2.8.7/cmake.html#command:cmake_minimum_required
COMP: Erroneous closing ')'

The refactoring for including modules for BRAINSTools
erroneously added an extra ')' on some include lines.
ENH: Add ANTs with PointSetMetric options.
ENH: Modified ignore statements for builds.
COMP: Fixes tests by explicitly specifying list of ITK IO components

Since ITK IO factory are not explicitly instantiated in the code, this
commit explicitly set the list "ITK_IO_MODULES_USED" for each
sub-project.

In case the sub-project was already specifying some ITKIO* component in
his regular list, care has been taken to make sure they are not duplicated.

Remarks:

(1) The list has been copied from Slicer own requirement
and probably not all sub-projects require the complete list. For sake
of correctness, it could make sense to revisit each list and trim
the ITKIO components that are not relevant.

(2) Ideally, the documentation of each module should specify which file
format are supported. An idea would be to generate the documentation
based on the list of ITKIO specified in each CMakeLists.txt.

(3) Looking at the "diff", you may notice that the
variable "${ITK_IO_MODULES_USED}" is not systematically appended to
the list of components, this is explained because previous commit 6e8b92e7
was already specifying it due to copy/paste "mistake".
Merge pull request #117 from jcfr/update-itk-components-to-include-io

COMP: Fixes tests by explicitly specifying list of ITK IO components
Revert "COMP: Fixes tests by explicitly specifying list of ITK IO components"

This reverts commit 10b1f22a29f12b7e7edac6ade160ed0ea4e94804.
Revert "COMP: Erroneous closing ')'"

This reverts commit 07000f09095daf093693733466079e0ae5c3c898.
Revert "COMP: Move ITK find_package calls into each sub-project."

This reverts commit 6e8b92e794305d8f49cbc22d318875162169901f.
Merge pull request #118 from jcfr/revert-find-package-in-every-sub-projects

Revert find package in every sub projects
COMP: Fix baseline for BRAINSABC test.
ENH: Update ants with merged compiler changes.
COMP: Attempting to resolve dashboard warnings.

This commit uses the CTestCustom at both the BRAINSTools and SuperBuild directory levels.
ENH: itkMultiLabelSTAPLEImageFilter.h is now part of ITK

The itkMultiLabelSTAPLEImageFilter is now a native part of ITK
and does not require internally maintained files.
COMP: Remove duplicate files from ITK

Files that are standard parts of ITK are removed to improve build.
ENH: Fix ITKv4 build options for VTK support.
BUG: Remove unconditional debug printing.

There was code that was performing unconditional debug transform writing
in ITK.
COMP: Order of variable processing was incorrect

The items for VTK dependancies of ITK for ITKVtkGlue were not correctly
ordered for operations to succeed.

VTK needed to be added to the dependancy list, then the superbuild
calls needed to be made, then the ITK build configuration of VTK variables
needed to be added.
BUG: for NrrdToFSL, generate Bval/Bvec filenames from NIfTI name if necessary