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

Fix/filter modal energy

Fix bug with uninitialized variable in FilterModalEnergy.

See merge request !427

Add regression tests for PETSc

This MR adds some regression tests for PETSc and fixes issues with parallel builds when compiling PETSc as a third-party library.

See merge request !429