STYLE: Make style compatible with cmake

The cmake convensions dictate the style of
cmake directives as being lower case, and
end of blocks should not have conditional
clause in them.

\#!/bin/bash

\#\#- Remove CMake-language block-end command arguments
\#\#-
\#\#- Ancient versions of CMake required else(), endif(), and similar
block
\#\#- termination commands to have arguments matching the command starting
the
\#\#- block.  This is no longer the preferred style.
\#\#-
\#\#- NOTE: MUST USE GNU compliant version of sed
\#\#- Run the following shell code:

for c in else endif endforeach endfunction endmacro endwhile; do
    echo 's/\b'"$c"'\(\s*\)(.\+)/'"$c"'\1()/'
    done >convert.sed \
      && git ls-files -z -- bootstrap '*.cmake' '*.cmake.in'
      '*CMakeLists.txt' \
           | xargs -0 gsed -i -f convert.sed \
           && rm convert.sed

\#!/bin/bash

\#Convert CMake-language commands to lower case

\#Ancient CMake versions required upper-case commands.  Later command
\#names became case-insensitive.  Now the preferred style is lower-case.

\#Run the following shell code:
\#\# NOTE: MUST USE GNU compliant version of sed
cmake --help-command-list \
| grep -v "cmake version" \
| while read c; do
    echo 's/\b'"$(echo $c | tr '[:lower:]'
    '[:upper:]')"'\(\s*\)(/'"$c"'\1(/g'
      done >convert.sed \
      && git ls-files -z -- bootstrap '*.cmake' '*.cmake.in'
      '*CMakeLists.txt' \
         | xargs -0 gsed -i -f convert.sed \
        && rm convert.sed
COMP: Reduce the number of exernal data fetch targets

Make one BRAINSTools project rather than many small projects.
COMP: Simplify building complexity

This is a heavy handed approach to resolving
a dependancy issue that prevented data
from being downloaded during the build
for BRAINSConstellationDetector.  The
dependancies were very complicated, so
I removed nearly all of the sub-projects
so that there are fewer relationships to
track down.
COMP: Remove conditional running of tests.
COMP: Clean up compilation cruft.
COMP: Attempt ordering change for build debugging.
COMP: Turn off BRAINSCut failures, fix ImageCalculatorFailures.
COMP: Clean up build process.
COMP: Remove setting of default CMake variable project_name
ENH: Clean up build scripts for clarity.
ENH: Added short workup test.
BUG: logical bug using the --doshort flag.
BUG: Fix DB initialization problem.
ENH: Suppress SEM warning about increases required alignment
BUG:  Number of threads was not being properly respected

Whatever then enduser requests for number of threads
on the command line should be respected, no matter what
the environmental variables are set to.
Merge pull request #115 from dmwelch/posteriorConvertBugFix

BUG: Posterior convert test data fix
ENH: Create better measurements csv file.
ENH: Put forceful upperlimit on memory use

To prevent oversubscription of the available memory you have to specify your requirements. If the machines runs out of memory and starts to swap all running job will slow down significantly. The first one is h_vmem. This is the upper limit for your application. If the job uses more it will be killed or it gets a memory allocation failure. The system limit for h_vmem is the size of the physical memory.
ENH: Re-add FreeSurfer to analysis.
ENH: Fine Tune Autoworkup parameters.