Place all dynamicalModel related into separate folder.
SceneElements now has just the tangable and intangable objects.

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.

Replace int by size_t in pbdModel
Rename constraintProjection to projectConstraints

Clean the pbdState to just have body states.
All the physics related parameters, time step size and time
integration routines are moved to pbdModel

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

Make a base class for problem state. All math models uses states that are derived from this class.
Rename ProblemState class to DeformableBodyState
Rename positionBasedModel to positionBasedDynamicsModel
Replace raw pointers with smart pointers in pbdModel class
rename class functions in pbdModel
pbdState: move function definitions to .ccp & replace int by size_t

Make locals const where ever possible in PBD constraint classes
Create separate files for each of PBD constraint classes

Move the implementation to .cpp for ProblemState class.
Adds missing comments for functions in ProblemState class.
Make DynamicObject derive from collidableObject rather than sceneObject.

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

We are still wondering how to store/apply our geometries.
Having yet another interface to only wrap the API to
transform the geometry is not needed: we can directly
call them on the geometry themselves for more transparency
on what geometry is being updated.

This will be investigated later on when we will work with
rigib body dynamics.

Colliding geometry is only in CollidingObject.

To do this, we also had to :
- have PbdObject inherit CollidingObject (in the future
there should not be a distinct object class just for Pbd :
there should just be dynamical objects that can use
different models, like Pbd or FEM)
- remove useless checks when creating interactions: even
two colliding objects (not dynamic, aka static) could
be interacting if they are both controlled by devices

Returns master geometry, defined master in the
geometry maps of the objects. Physic geometry will
drive the changes to the colliding geometry, which
will drive the changes to the visual geometry

- Get rid of scaling in constructor (too many parameters,
why choose scaling and not others? Use setTranslationScaling
instead)

- No more default nullptr value for deviceClient in controller
constructor

convert tabs to 4 spaces

Was triggered build errors on windows due to
std:to_string

The offset should only be defined at the
controller level

Also remove useless include in VRPNDeviceServer

Co-authored by: Nicholas Milef <milefn@rpi.edu>

1) DeviceClient : not a module anymore, only stores device info
and holds callbacks

2) VRPNDeviceClient : subclasses DeviceClient AND Module, to
conserve the ability to run multiple clients in parallel with
a VRPN server

3) HDAPIDeviceServer : new module that manages the HDAPIDevice
clients execution, which need to be made sequentially. Also helps
managing a unique hdScheduler.

4) HDAPIDeviceClient : lets the HDAPIDeviceServer handle the
hdScheduler. Also makes use of hdMakeCurrentDevice.

5) SimulationManager : refactor to run modules instead of
deviceservers or deviceclients

6) Sandbox : use new simulationManager API to add modules

- 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.

Enforces style and place holders for comments in the pbd related code files

Adds basic plot generator scripts for vectors for Matlab and Matlibplot

Style enforcement and add comments over the entire code

Adds updateFunction to the NL system. Some style cleanup.

Trigger compilation error on macOSx