Enforces license header and the rest of configuration options. To enable it,
manually run SetupForDevelopment.sh and enable uncrustify during configure.
Also provided is default configuration file to be consulted when a new
option is needed. This file has explanations for all the options.

Also, some source code files have been modified to prevent ugly auto-reformatting.

Move the Linear Projection Constraints (LPC) from the nonlinear system to CG solver for simplicity.
LPC are only used in CG.

- Geometry class does not have a position, orientation, scaling combination
anymore, but a rigid transformation (translation + rotation) as well as a
separate uniform scaling.
- The value of that transformation can be changed using setTranslation(),
setRotation(), and setScaling().
- scale(), translate(), and rotate() are utility functions which behavior
vary based on the parameter TransformType: ConcatenateToTransform, the
default value, will concatenate transformations to the rigid transform and
signals that the transform has been modified; ApplyToData directly enforces
the transformation given to the internal data of the geometry, and signals
that the data has been modified (useful to enforce offsets at the beginning
of the simulation to avoid concatenating that offset continuously).
- A new base class AnalyticalGeomerty is created for Capsule, Plane, Cube
and Sphere. It wraps the common attributes to those geometries: a position
and an orientation axis. The values of those properties after the transform
is applied are also stored to avoid redundant computations.
- Subclasses of AnalyticalGeometry often show properties related to size:
width, radius, length, etc. Those have their post-transform sibling also.
- The Plane has a Normal API which simply wraps the AnalyticalGeometry
orientation axis.
- The mesh base class also keeps track of a post-transform value for the
vertex positions.
- Those internal data properties can be set with regular setting methods,
which also signals that the internal data has been modified.
- Get methods for those properties have a behavior which vary based on
the parameter DataType: PostTransform is the default value, and it will
return the post transform data, computing it by applying the transform if
it was not yet done.
- CollisionDetection classes are updated to use that post-transform data
- RenderDelegates are updated to update their internal data only when
the geometry data has been modified (use VTK sources and transform filter),
as well as the rigid transform when that one has been modified also.
- Maps, Controllers, and tests are updated to use the correct API:
set translation and rotation and not position/orientation.
- Update Geometry and Plane test to take into account the change of API:
getRotation is now returning a Mat3d instead of a quaternion for less
operations, and getNormal will return a normalized vector even if the one
set was not normalized. Use `isApprox` to allow for low variability.
- Update API in sandbox example
- Got rid of the vertexDisplacements variable in the Mesh class, difference
between the vertexPosition and the initialVertexPositions: it was requiring
additional bookeeping which was not necessary

Co-Authored-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>
Signed-off-by: Alexis Girault <alexis.girault@kitware.com>

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

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

The current integration of UPS within the module class did not allow
to display the UPS value in any easy and standardized way.

This commits simplifies the Module class by removing its dependency to
the UPSCounter class, and shows how to easily query the UPS using the
callback mechanism on any module (here: sceneManager for pbd physics and
fem physics examples).

Allows to set up custom behaviors in all subclasses of the Module class,
at:
- prior to initialization
- after initialization
- prior to update
- after update
- prior to clean up
- after clean up

Improve the testTwoFalcons example in Sandbox to quickly illustrate how
to simply setup a logger for a deviceclient using those features.

* Remove camera controller from test since already shown in
testCameraController, to be able to test with just two falcons
* Update some initial geometry and camera positions
* remove imstk namespace since using namespace imstk in sandbox

/*=========================================================================

   Library: iMSTK

   Copyright (c) Kitware, Inc. & Center for Modeling, Simulation,
   & Imaging in Medicine, Rensselaer Polytechnic Institute.

   Licensed under the Apache License, Version 2.0 (the "License");
   you may not use this file except in compliance with the License.
   You may obtain a copy of the License at

      http://www.apache.org/licenses/LICENSE-2.0.txt

   Unless required by applicable law or agreed to in writing, software
   distributed under the License is distributed on an "AS IS" BASIS,
   WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   See the License for the specific language governing permissions and
   limitations under the License.

=========================================================================*/

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

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

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

Adds utility functions for creating scene objects with commonly used
call patterns

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

Generalizes linear projection constraints implementation.
Modifies testDeformableBody example to test the changes.

DATA_ROOT_PATH did not exist since the introduction of external data.
Save screenshots in runtime directory instead.

Correct warning: extra tokens at end of #else directive in
testCameraController

Mistakes following the addition of more ExternalData from merged PR:
iMSTK/iMSTK!135

CDash: http://my.cdash.org/viewBuildError.php?buildid=1143408

* Add data needed for the examples inside Sandbox
    except ETI & textures
* Remove condition on DATA_ROOT_PATH since the user doesn't have to specify it
* Rename DATA_ROOT_PATH to iMSTK_DATA_ROOT according to 267b7f72

The device tracker stays up-of-date at all frames and is fixed by
setting m_trackingDataUptoDate to false at the end of the frame

Download Data from Girder according to data key files contained in iMSTK/Data

This uses ExternalData.cmake (Requires CMake >= 2.8.11 release).

Add TEST: Add ExternalDataTest to verify downloaded files from Girder
* Be sure the data requiered for the test is not there (delete it)
* Add the imstk_add_data(${target} ${data_list}) function in CMakeList.txt
which calls ExternalData_expand_arguments().
* It downloads the data provided by the data_list (relative path from
iMSTK/Data)

Add DOC: Add documentation on ExternalData Management
* How to add data to iMSTK from Grider
* Update data
* Use data

Also correct indentation in Pbd class.

Create a tool with two jaws and a shaft. The controller
use its DeviceTracker to update the three objects

* 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 can be set as current in the simulation manager using the scene
pointer in addition to its name.

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).

DATA_ROOT_PATH is used to quickly define the root path
for all your ressources in the Sandbox example. Its value
will therefore vary for every user, which is why it should
not be commited.

This commit adds comments explaining not to commit changes
to this line, as well as how to commit part of a file only,
and displays an error when the path is not set locally.

Written-by: Sreekanth Arikatla <sreekanth.arikatla@kitware.com>