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Conflicts:
	solvers/IncNavierStokesSolver/AdvectionTerms/AdjointAdvection.cpp
	solvers/IncNavierStokesSolver/AdvectionTerms/AdjointAdvection.h

dont overwrite chk files if the solver was restarted

in case f a restart, read the number from the restart file and use this as starting point for the next chk files, so that when restarting from foo_215.chk, the first chk file written is not foo_0.chk but foo_215_0.chk (which contains the initial conditions and should in most cases be identical to foo_215.chk). The next file will be foo_216.chk with the new timestep.

In case foo_215_0.chk already exists, we write foo_215_1.chk and so on.

The filters still overwrite everything, maybe we should change that too?

See merge request !707

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