fix/linearise

This MR fixes the linearise threshold routine which was being far too over aggressive in the linearisation of prism elements.
This is because it was measuring linear deformation when considering the quality, this has now been fixed.

See merge request !717

# Conflicts:
#   utilities/NekMesh/ProcessModules/ProcessLinear.cpp

Feature/helmsmooth3D

This MR enables the hemholtz smoother for 3D problems

It also activates PETSc MUMPS support when a Fortran compiler is present because currently, only direct solvers can reliably handle the resulting linear system.

See merge request !714

feature/mc-extrude

Simple module that extrudes a 2D mesh in the z direction

Works for triangles (prisms) and quads (hexs) and propagates curvature through the extrusion.

See merge request !715

# Conflicts:
#   CHANGELOG.md

feature/linearise_extract

Small MR that adds the ability to dump the elements which were touched by the linearise module for visualisation.

See merge request !712

Fix multiple xml files in FieldConvert



See merge request !705

fix history points precision

this MR make the historypoints filter actually use the full field width

See merge request !706

Feature/ann_remove

Removes the dependency on the external library in favor of using boost::geometry. This may be noticeable slower in tree construction but has many more features and doesnt require another third party dependency, meaning that the massive speed up to the spherigon and isocontour routines can be provided in the default versions. 

The new version of the mesh generation routines dont require ann either.

See merge request !703

Tidy compressible solver

This MR makes several changes which I believe make the code for the compressible solver a lot more organised. I originally intended to work on the efficiency of the solver, but I only made a few changes towards this. The main changes are:

- Move boundary conditions to separate class using factory

- Move functions for converting variables (e.g. GetPressure) to a separate auxiliary class

- Remove the ProblemType option and have RinglebFlow and IsentropicVortex as separate equation systems derived from Euler

- Try to be more consistent about what should  be in the CompressibleFlowSystem base class and what is specific to the particular equations

- Rewrite the GetFluxVector functions in a more compact form, which depends on the problem dimension only in the loop limits

- Allow passing Fwd and Bwd trace space to Advection and Diffusion operators as optional parameters. If these parameters are not set they are calculated as usual, but using them helps in saving some communication cost by reusing the values passed to the advection in the diffusion (perhaps a better condition is required to determine when to precompute these values).

I also implemented a semi-implicit DG/HDG for the unsteady advection diffusion, which seems to be working fine.

See merge request !684

Add support for binary output to Tecplot output

This MR adds support for binary Tecplot fields in the `.plt` format for both normal tensor/collapsed-coordinate output and equispaced output. In addition, when running in parallel, FieldConvert will now produce a single `.plt` instead of multiple file outputs per partition.

See merge request !683

Use new boundary functions in Extrapolate

This will address issue #13. Basically, this involves modifying `Extrapolate.cpp` to use the new functions from MultiRegions for working with boundaries, leading to a much simpler implementation.

See merge request !579

Add Nek5000 mesh and field conversion

This MR adds new modules for NekMesh and FieldConvert to support input from Nek5000 based format, which is a tensor-product GLL hexahedra and quadrilateral code. The mesh format is similar to the Nektar rea format but is sufficiently different to warrant its own input module. This MR also adds support for zlib-encoded input and output for NekMesh to reduce file size of test files.

There are some caveats:

- Field input is restricted to that written by Nek5000 in parallel - serial output is not supported.
- Mesh files only support very basic boundary conditions; walls and periodic conditions (there is no support for the `.usr` files that define time-dependent BCs). 

See merge request !680

Restart for filters based on FilterFieldConvert

This MR adds support to use a restart file for filters derived from FilterFieldConvert (e.g. averaged fields). 

See merge request !678