Merge remote-tracking branch 'andreiled/dev' into dev. Conflicts resolved manually:
	.gitignore
	system/GCMException.h
Cas reader minor update to use new Node methods
Dump node flags when writing a VTK snapshot
 Changes to be committed:
	modified:   datatypes/Node.h
	modified:   system/VTKSnapshotWriter.cpp
	modified:   system/VTKSnapshotWriter.h
Set access for methods getFlags and setFlags to private, only friendly class
VTKSnapshotWriter will be able to access them.
 Changes to be committed:
	modified:   datatypes/Node.h
Move everything to ./gcm to simplify code structure for zsph integration
Merge remote-tracking branch 'upstream/dev' into dev
Ignore files list
 Changes to be committed:
	modified:   .gitignore
Merge branch 'dev' into zsph-gcm-dev

Resolved Conflicts:
	.gitignore
	gcm/meshtypes/TetrMesh_1stOrder.cpp
	gcm/system/GCMException.h

CMakeModules as well as files shared between gcm3d and spgcm3d projects
moved to spgcm directory. The project is now to be built from spgcm directory.

 Changes to be committed:

	modified:   .gitignore
	deleted:    CMakeLists.txt
	renamed:    README -> gcm/README
	renamed:    datatypes/Basis.h -> gcm/datatypes/Basis.h
	renamed:    datatypes/ContactData.h -> gcm/datatypes/ContactData.h
	renamed:    datatypes/ElasticMatrix3D.cpp -> gcm/datatypes/ElasticMatrix3D.cpp
	renamed:    datatypes/ElasticMatrix3D.h -> gcm/datatypes/ElasticMatrix3D.h
	renamed:    datatypes/ElasticNode.cpp -> gcm/datatypes/ElasticNode.cpp
	renamed:    datatypes/ElasticNode.h -> gcm/datatypes/ElasticNode.h
	renamed:    datatypes/Element.cpp -> gcm/datatypes/Element.cpp
	renamed:    datatypes/Element.h -> gcm/datatypes/Element.h
	renamed:    datatypes/MeshOutline.h -> gcm/datatypes/MeshOutline.h
	renamed:    datatypes/Node.cpp -> gcm/datatypes/Node.cpp
	renamed:    datatypes/Node.h -> gcm/datatypes/Node.h
	renamed:    datatypes/Tetrahedron.cpp -> gcm/datatypes/Tetrahedron.cpp
	renamed:    datatypes/Tetrahedron.h -> gcm/datatypes/Tetrahedron.h
	renamed:    datatypes/Tetrahedron_1st_order.cpp -> gcm/datatypes/Tetrahedron_1st_order.cpp
	renamed:    datatypes/Tetrahedron_1st_order.h -> gcm/datatypes/Tetrahedron_1st_order.h
	renamed:    datatypes/Triangle.cpp -> gcm/datatypes/Triangle.cpp
	renamed:    datatypes/Triangle.h -> gcm/datatypes/Triangle.h
	renamed:    datatypes/matrixes.cpp -> gcm/datatypes/matrixes.cpp
	renamed:    datatypes/matrixes.h -> gcm/datatypes/matrixes.h
	renamed:    main.cpp -> gcm/main.cpp
	renamed:    meshtypes/Mesh.cpp -> gcm/meshtypes/Mesh.cpp
	renamed:    meshtypes/Mesh.h -> gcm/meshtypes/Mesh.h
	renamed:    meshtypes/TetrMesh.cpp -> gcm/meshtypes/TetrMesh.cpp
	renamed:    meshtypes/TetrMesh.h -> gcm/meshtypes/TetrMesh.h
	renamed:    meshtypes/TetrMesh_1stOrder.cpp -> gcm/meshtypes/TetrMesh_1stOrder.cpp
	renamed:    meshtypes/TetrMesh_1stOrder.h -> gcm/meshtypes/TetrMesh_1stOrder.h
	renamed:    methods/BorderCalculator.cpp -> gcm/methods/BorderCalculator.cpp
	renamed:    methods/BorderCalculator.h -> gcm/methods/BorderCalculator.h
	renamed:    methods/ContactCalculator.cpp -> gcm/methods/ContactCalculator.cpp
	renamed:    methods/ContactCalculator.h -> gcm/methods/ContactCalculator.h
	renamed:    methods/NumericalMethod.cpp -> gcm/methods/NumericalMethod.cpp
	renamed:    methods/NumericalMethod.h -> gcm/methods/NumericalMethod.h
	renamed:    methods/TetrMethod_Plastic_1stOrder.cpp -> gcm/methods/TetrMethod_Plastic_1stOrder.cpp
	renamed:    methods/TetrMethod_Plastic_1stOrder.h -> gcm/methods/TetrMethod_Plastic_1stOrder.h
	renamed:    methods/TetrNumericalMethod.cpp -> gcm/methods/TetrNumericalMethod.cpp
	renamed:    methods/TetrNumericalMethod.h -> gcm/methods/TetrNumericalMethod.h
	renamed:    methods/VolumeCalculator.cpp -> gcm/methods/VolumeCalculator.cpp
	renamed:    methods/VolumeCalculator.h -> gcm/methods/VolumeCalculator.h
	renamed:    methods/border/ExternalForceCalculator.cpp -> gcm/methods/border/ExternalForceCalculator.cpp
	renamed:    methods/border/ExternalForceCalculator.h -> gcm/methods/border/ExternalForceCalculator.h
	renamed:    methods/border/ExternalValuesCalculator.cpp -> gcm/methods/border/ExternalValuesCalculator.cpp
	renamed:    methods/border/ExternalValuesCalculator.h -> gcm/methods/border/ExternalValuesCalculator.h
	renamed:    methods/border/ExternalVelocityCalculator.cpp -> gcm/methods/border/ExternalVelocityCalculator.cpp
	renamed:    methods/border/ExternalVelocityCalculator.h -> gcm/methods/border/ExternalVelocityCalculator.h
	renamed:    methods/border/FixedBorderCalculator.cpp -> gcm/methods/border/FixedBorderCalculator.cpp
	renamed:    methods/border/FixedBorderCalculator.h -> gcm/methods/border/FixedBorderCalculator.h
	renamed:    methods/border/FreeBorderCalculator.cpp -> gcm/methods/border/FreeBorderCalculator.cpp
	renamed:    methods/border/FreeBorderCalculator.h -> gcm/methods/border/FreeBorderCalculator.h
	renamed:    methods/contact/AdhesionContactCalculator.cpp -> gcm/methods/contact/AdhesionContactCalculator.cpp
	renamed:    methods/contact/AdhesionContactCalculator.h -> gcm/methods/contact/AdhesionContactCalculator.h
	renamed:    methods/volume/SimpleVolumeCalculator.cpp -> gcm/methods/volume/SimpleVolumeCalculator.cpp
	renamed:    methods/volume/SimpleVolumeCalculator.h -> gcm/methods/volume/SimpleVolumeCalculator.h
	renamed:    rheotypes/RheologyCalculator.cpp -> gcm/rheotypes/RheologyCalculator.cpp
	renamed:    rheotypes/RheologyCalculator.h -> gcm/rheotypes/RheologyCalculator.h
	renamed:    rheotypes/VoidRheologyCalculator.cpp -> gcm/rheotypes/VoidRheologyCalculator.cpp
	renamed:    rheotypes/VoidRheologyCalculator.h -> gcm/rheotypes/VoidRheologyCalculator.h
	renamed:    system/BorderCondition.cpp -> gcm/system/BorderCondition.cpp
	renamed:    system/BorderCondition.h -> gcm/system/BorderCondition.h
	renamed:    system/BruteforceCollisionDetector.cpp -> gcm/system/BruteforceCollisionDetector.cpp
	renamed:    system/BruteforceCollisionDetector.h -> gcm/system/BruteforceCollisionDetector.h
	renamed:    system/CollisionDetector.cpp -> gcm/system/CollisionDetector.cpp
	renamed:    system/CollisionDetector.h -> gcm/system/CollisionDetector.h
	renamed:    system/CollisionDetectorForLayers.cpp -> gcm/system/CollisionDetectorForLayers.cpp
	renamed:    system/CollisionDetectorForLayers.h -> gcm/system/CollisionDetectorForLayers.h
	renamed:    system/ContactCondition.cpp -> gcm/system/ContactCondition.cpp
	renamed:    system/ContactCondition.h -> gcm/system/ContactCondition.h
	renamed:    system/CylTest.cpp -> gcm/system/CylTest.cpp
	renamed:    system/CylTest.h -> gcm/system/CylTest.h
	renamed:    system/DataBus.cpp -> gcm/system/DataBus.cpp
	renamed:    system/DataBus.h -> gcm/system/DataBus.h
	renamed:    system/GCMException.cpp -> gcm/system/GCMException.cpp
	renamed:    system/GCMException.h -> gcm/system/GCMException.h
	renamed:    system/GCMStresser.cpp -> gcm/system/GCMStresser.cpp
	renamed:    system/GCMStresser.h -> gcm/system/GCMStresser.h
	renamed:    system/LineSnapshotWriter.cpp -> gcm/system/LineSnapshotWriter.cpp
	renamed:    system/LineSnapshotWriter.h -> gcm/system/LineSnapshotWriter.h
	renamed:    system/Logger.cpp -> gcm/system/Logger.cpp
	renamed:    system/Logger.h -> gcm/system/Logger.h
	renamed:    system/LoggerUser.cpp -> gcm/system/LoggerUser.cpp
	renamed:    system/LoggerUser.h -> gcm/system/LoggerUser.h
	renamed:    system/Logging.h -> gcm/system/Logging.h
	renamed:    system/SnapshotWriter.cpp -> gcm/system/SnapshotWriter.cpp
	renamed:    system/SnapshotWriter.h -> gcm/system/SnapshotWriter.h
	renamed:    system/Stresser.cpp -> gcm/system/Stresser.cpp
	renamed:    system/Stresser.h -> gcm/system/Stresser.h
	renamed:    system/TaskPreparator.cpp -> gcm/system/TaskPreparator.cpp
	renamed:    system/TaskPreparator.h -> gcm/system/TaskPreparator.h
	renamed:    system/TetrMeshSet.cpp -> gcm/system/TetrMeshSet.cpp
	renamed:    system/TetrMeshSet.h -> gcm/system/TetrMeshSet.h
	renamed:    system/Utils.cpp -> gcm/system/Utils.cpp
	renamed:    system/Utils.h -> gcm/system/Utils.h
	renamed:    system/VTKSnapshotWriter.cpp -> gcm/system/VTKSnapshotWriter.cpp
	renamed:    system/VTKSnapshotWriter.h -> gcm/system/VTKSnapshotWriter.h
	renamed:    system/VoidCollisionDetector.cpp -> gcm/system/VoidCollisionDetector.cpp
	renamed:    system/VoidCollisionDetector.h -> gcm/system/VoidCollisionDetector.h
	renamed:    system/areas/Area.cpp -> gcm/system/areas/Area.cpp
	renamed:    system/areas/Area.h -> gcm/system/areas/Area.h
	renamed:    system/areas/BoxArea.cpp -> gcm/system/areas/BoxArea.cpp
	renamed:    system/areas/BoxArea.h -> gcm/system/areas/BoxArea.h
	renamed:    system/areas/CylinderArea.cpp -> gcm/system/areas/CylinderArea.cpp
	renamed:    system/areas/CylinderArea.h -> gcm/system/areas/CylinderArea.h
	renamed:    system/areas/SphereArea.cpp -> gcm/system/areas/SphereArea.cpp
	renamed:    system/areas/SphereArea.h -> gcm/system/areas/SphereArea.h
	renamed:    system/forms/PulseForm.cpp -> gcm/system/forms/PulseForm.cpp
	renamed:    system/forms/PulseForm.h -> gcm/system/forms/PulseForm.h
	renamed:    system/forms/StepPulseForm.cpp -> gcm/system/forms/StepPulseForm.cpp
	renamed:    system/forms/StepPulseForm.h -> gcm/system/forms/StepPulseForm.h
	renamed:    system/quick_math.cpp -> gcm/system/quick_math.cpp
	renamed:    system/quick_math.h -> gcm/system/quick_math.h
	renamed:    builddeps.sh -> gcm/tools/builddeps.sh
	renamed:    tools/create_cube.c -> gcm/tools/create_cube.c
	renamed:    tools/create_layer.c -> gcm/tools/create_layer.c
	renamed:    tools/plot2d.cpp -> gcm/tools/plot2d.cpp
	renamed:    setenv.sh -> gcm/tools/setenv.sh
	renamed:    unittests/checkCoordDerivativesCalc.cpp -> gcm/unittests/checkCoordDerivativesCalc.cpp
	renamed:    unittests/checkElasticMatrix3D.cpp -> gcm/unittests/checkElasticMatrix3D.cpp
	renamed:    unittests/checkFindOwnerTetrAdvancedImpl.cpp -> gcm/unittests/checkFindOwnerTetrAdvancedImpl.cpp
	new file:   spgcm/CMakeLists.txt
	renamed:    CMakeModules/FindGSL.cmake -> spgcm/CMakeModules/FindGSL.cmake
	renamed:    CMakeModules/FindLOG4CXX.cmake -> spgcm/CMakeModules/FindLOG4CXX.cmake
	renamed:    CMakeModules/FindMPI.cmake -> spgcm/CMakeModules/FindMPI.cmake
	renamed:    CMakeModules/FindTinyXML.cmake -> spgcm/CMakeModules/FindTinyXML.cmake
	modified:   spgcm/cmd/GenerateAction.cpp
	modified:   spgcm/cmd/GenerateAction.h
	renamed:    log4cxx.properties -> spgcm/log4cxx.properties
	modified:   spgcm/spgcm_main.cpp
	deleted:    todo.txt
	deleted:    unittests/Makefile