Fix/pkg cmake3 take2

See merge request !436

Fix/pkg cmake3

This MR fixes the packaging system for CMake 3.0

See merge request !435

Fix/docs

See merge request !434

Fix/cpc review

This MR adds modifications to the code as requested by the CPC paper review.

See merge request !422

Fix/warnings

This MR fixes a number of compiler warnings such as unused variables and variables which might be used potentially uninitialised.

See merge request !432

Fix/for visit

This MR fixes a number of issues relating to the code and the build system to allow a Nektar++ reader to be compiled as a third-party library for the VisIt visualisation package.

See merge request !419

Fix OS X warning with clang, refactor weighting function slightly to remove commented out lines and code duplication

Feature/shallow water solver

Added a DG solver for the Boussinesq equations of Peregrine (constant depth case) to the ShallowWaterSolver. Added an example case of a solitary wave.

See merge request !431

Conflicts:
	cmake/ThirdPartyBoost.cmake
	cmake/ThirdPartyPETSc.cmake

Changes to be committed:
	new file:   solvers/ShallowWaterSolver/Examples/Cylinder_Boussinesq_DG.xml

On branch feature/ShallowWaterSolver
Changes to be committed:
	modified:   solvers/ShallowWaterSolver/CMakeLists.txt
	new file:   solvers/ShallowWaterSolver/EquationSystems/NonlinearPeregrine.cpp
	new file:   solvers/ShallowWaterSolver/EquationSystems/NonlinearPeregrine.h
	modified:   solvers/ShallowWaterSolver/EquationSystems/NonlinearSWE.cpp

Feature/field convert equi output

See merge request !421

Fix/session name prepartitioned

This MR includes the following:
* Fixes the determination of the session name from pre-partitioned mesh directories.
* Remove code duplication of the determination of the session name into a separate function.
* Removes the m_filename parameter (since it no longer makes sense when we can load multiple files) from the session reader.
* Improves the error messages in parsing parameters and solver info to show the erroneous XML element.
* Fixes a segfault if a parameter such as "Test = 1 2" is given.
* Detect when boundary conditions with same ID appears multiple times.

This fixes tickets #148 and #122.

See merge request !426

Allow filename variable remapping

This MR adds the option to remap variable names inside files to different names in XML functions. For example, `IncNavierStokesSolver` fields containing `u,v,w,p` can be mapped to linear advection variables `Vx,Vy,Vz` using the syntax:

```xml
<FUNCTION NAME="AdvectionVelocity">
  <F VAR="Vx,Vy,Vz" VALUE="file.fld:u,v,w" />
</FUNCTION>
```

See merge request !428