Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1552

The implementation now correspond to the definitions in the readily
available reference:

http://personalpages.manchester.ac.uk/staff/david.d.apsley/specturb.pdf

in which a large number of linear and non-linear models are presented in
a clean and consistent manner.  This has made re-implementation and
checking far easier than working from the original references which anyway
are no longer available for the LienCubicKE and ShihQuadraticKE models.

which takes the inner product of a symmTensor with itself and returns a symmTensor

Resolves bug-report http://openfoam.org/mantisbt/view.php?id=1548

Resolves issues with probes and findRefCell for meshes in which all cell face-pyramids are positive.

This is an experimental feature demonstrating the potential of MULES to
create bounded solution which are 2nd-order in time AND space.

Crank-Nicolson may be selected on U and/or alpha but will only be fully
2nd-order if used on both within the PIMPLE-loop to converge the
interaction between the flux and phase-fraction.  Note also that
Crank-Nicolson may not be used with sub-cycling but all the features of
semi-implicit MULES are available in particular MULESCorr and
alphaApplyPrevCorr.

Examples of ddt specification:

ddtSchemes
{
    default         Euler;
}

ddtSchemes
{
    default         CrankNicolson 0.9;
}

ddtSchemes
{
    default         none;
    ddt(alpha)      CrankNicolson 0.9;
    ddt(rho,U)      CrankNicolson 0.9;
}

ddtSchemes
{
    default         none;
    ddt(alpha)      Euler;
    ddt(rho,U)      CrankNicolson 0.9;
}

ddtSchemes
{
    default         none;
    ddt(alpha)      CrankNicolson 0.9;
    ddt(rho,U)      Euler;
}

In these examples a small amount of off-centering in used to stabilize
the Crank-Nicolson scheme.  Also the specification for alpha1 is via the
generic phase-fraction name to ensure in multiphase solvers (when
Crank-Nicolson support is added) the scheme is identical for all phase
fractions.

Uses a form of the Euler equation in which only variation along the streamlines is considered

Pass the phase-name through hierarchy
Add phase-name to variables
Split basicCombustionMixture
Update applications accordingly

Needed to create generic compressible turbulence model library

Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1534

compressibleInterDyMFoam and interPhaseChangeDyMFoam: cache divU before time advancement to ensure the old-time meshPhi are used to make phi absolute
Resolves bug-report http://www.openfoam.org/mantisbt/view.php?id=1531

refineWallLayer: Rationalize and add support for operating on a list of patch name regular expressions
Resolves bug-report http://openfoam.org/mantisbt/view.php?id=1525

potentialFoam: Solve for velocity potential named Phi rather than using the pressure field for this purpose

The Phi field is read if available otherwise created automatically with
boundary conditions obtained automatically from the pressure field if
available (with optional name) otherwise inferred from the velocity
field.  Phi Laplacian scheme and solver specification are required.  See
tutorials for examples.

Use interFoam with fvOptions

Resolves bug-report http://openfoam.org/mantisbt/view.php?id=1382

Required change to IOobjectList to support the optional no-registration specification