Forces were wrongfully applied by the controllers onto the external
devices before the forces were computed.

- Velocity of particles should be updated only after collision being
  resolved.
- Rename from integrateVelocity() to updateVelocity() for pbdObject and
  pbdModel.

Adds deformable-rigid penalty collision handling. Unifies all the
penalty collision handling classes into one.

Co-Authored-by: Alexis Girault <alexis.girault@kitware.com>

* Rename TrackingController to DeviceTracker
* Have subclasses store a pointer to DeviceTracker instead
of inheriting it. This allows:
1. swapping the tracking controller at runtime
2. having multiple controllers control for the same scene object (eg: laparoscopic tool jaw)
* Add SceneObjectControllerBase to parent SceneObjectController
and other future object controllers
* Update tracking data only once per frame: if the same tracker
is used for multiple objects, it is updated only once per frame.
Each tracker is set to upToDate once the tracking data is updated
and offsets computed once at each frame. At the end of the frame
all the device trackers are set to be outOfDate.

Scene object controllers are now part of the scene. They are looped through
in the sceneManager to update the objects they contain.

This will allow extension to the case where multiple scene objects are
controlled by the same controller (eg: two-jawed laparoscopic tool).

Renames pbd constraint classes.
Renames the selfUpdate to updateGeometries

1. Adds self update to the scene objects. The objects now can update themselves instead of explicit way of updating in the sceneManager class.
2. Clear warnings in PbdVolumeeConstraint, DeformableModel, PbdModel, NewtonMethod classes
3. Clean the main() in the sandbox example

1. Seperate files for separate Pbd colliison constrain classes
2. Preincrement lop variables
3. Refactor collision constraint classes: remove raw pointers, using auto, style corrections
4. Move pbd constraints to seperate folder within constraint folder
5. Clears warnings in Physics module

1. Dynamical object classes are templated with the problem state
   (Deformable bodies use vectorized state. Pbd objects use pbdState.)
2. Pbd state is refactored to have only the current state
3. Rename deformableBodyState to VectorizedState which can be used in
   future by all the finite element and vectorized formulations
4. Remove unnecessary mappnig for the cloth example
5. Adds queries to sceneobject for visible, collidable and physics
6. Optional allocation of internal states for pbdState
7. Removes the specialized calls in the sceneManager::runModule.
   This will be further cleaned.
8. Correct ifdef in imstkNewmarkBeta.h

Rename DeformableBodyState to VectorizedState
Make the ifDefs consistent in style
Place and correct the headers in some files. This has to be done for all files at some point.

Adds a solver base class so that both nonlinear solvers and the pbd solver derives from it.
This simplifies the SceneManager::runModule()

SceneObjectController: similar to cameraController, it
subclasses trackingController to update the transformation
of an object master geometry, instead of updating itself.

SceneObject: similar to camera, has an interface to easily
setup a controller using a device client.

CollidingObject: stores the force vector that is to be
applied to the device.

SceneManager: make the API calls from controller instead
of object

convert tabs to 4 spaces

- Fix workflow for PBD in SceneManager.cpp. Add/modify related functions for
PbdObject/PbdRigidObject/VirtualCoupleingPBDObject. It should work for the
most general case where collision/physics/visual meshes are different from
each other.
- Add LineMesh class and LineMeshRenderDelegate. Add support for LineMesh
class in imstkGeometry, imstkMesh, imstkRenderDelegate.

- Fix a bug for computeBoundingBox() in imstkMesh.
- Fix a bug for applying mapping in TetraTriangleMap.
- Fix a bug for computing the center of tetra in TetraTriangleMap.

	-Create PbdRigidObject class for objects that are not deformable but need
	to interact with deformable pbd objects.
	-Create VirtualCouplingPbdObject class, which is inherted from
	PbdRigidObject and TrackingController. The physics and colliding
	geometry(mesh) need to be translate/rotate manually to interact
	with deformable objects, which is different from existing
	VirtualCouplingObject class.

Style enforcement and add comments over the entire code

Adds updateFunction to the NL system. Some style cleanup.

Move force models implementation to ccp files

Adds solver, maps to scene manager pipeline.
Enables different types of state updates.
Improves the example.

Maintain consistency in enum class object types
Create folders for time integrators and solvers

1. Merge CollidingSceneObject into SceneObject. SceneObject is now optionally viewable
and collideable but not movable. SceneObject class has all the functionality of a static object.
2. Rename imstkLigUtility to imstkLogger
3. Rename virtualCouplingObject to virtualToolObject
4. Consistency with brackets for imstk namespace
5. Move enums that  into imstk scope unless if the enum has no meaning outside the class

1) Change the interactionPair structure to save
only one collisiondata per structure, and inform
the collisionhandling of a "side" defining which
object it is handling, therefore which way it needs
to read the collisionData

2) Update MeshToMeshCD to properly populate data
based on 1.

Implement getInteractionPairList and getInteractionPairMap
in CollisionGraph for this.

1) for camera controller, setup offsets in initModule
based on the camera transform

2) for object controller, setup offset in sceneManager
initModule based on the object colliding geometry transform

This API allows the user to only worry about the geometries
and camera transforms, and let the controllers auto-init based
on that information when the simulation starts only.

Reset sceneManager loop delay to 0 (fast loop)
and remove LOG info to avoid too much printing.

Subclass of trackingcontroller and collidingobject

A surfaceMesh will not be automatically extracted when
reading a volumetricMesh due to the long time necessary
for that process, which will be improved later on.
(vtkDatasetSurfaceFilter is 100x faster)

The user will have to call computeAttachedSurfaceMesh to
extract the surface mesh from its volumetricMesh if he
needs it.