Feature/meshing release

This merge request is the massive clean up, reformatting and documenting (WIP) of the mesh generation routines.
This is the release candidate we can iterate on with smaller branches in the future.

See merge request !704

Feature/newhobcs

Added in a new convective like outflow boundary condition as well as a velocity correction scheme using a weak pressure Poisson equations. 

To complement this I have also tried to restructure the description in the user guide to use the Guermond and Shen approach to motivate both the standard velocity correction scheme and the weak pressure form.  

See merge request !713

Conflicts:
	CHANGELOG.md

Tidy linearised advection and fix full 3D

This MR simplifies the logic of `LinearisedAdvection::v_Advect`, reducing the dependency on the dimension and handling all components in a single loop. In doing so, I think this fixes the full 3D case, which was not working. Also, the gradient of the base flow is now computed in a separate function and stored in `m_gradBase`, avoiding the need to recompute this every time-step for steady base flows.

The adjoint advection is now derived from LinearisedAdvection, eliminating a lot of duplicate code. It only needs to redefine v_Advect, which now follows a similar structure to the new implementation from LinearisedAdvection.

See merge request !708

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