- The previous option 'write-nut' controlled the writing of turbulence
  nut, but other turbulence fields were always written.
  These have been shown to be a source of instability for many cases.

  This commit replaces the 'write-nut' option by a 'writeTurbulenceFields'
  option that controls the writing of all turbulence fields.
  If not set, only the velocity field is written.

  For compatibility, the old 'write-nut' option is still recognized
  but is redirected to 'writeTurbulenceFields'.

General:
    * -roots, -hostRoots, -fileHandler

Specific:
    * -to <coordinateSystem> -from <coordinateSystem>

- Display -help-compat when compatibility or ignored options are available

STYLE: capitalization of options text

- controlled by the the 'printExecutionFormat' InfoSwitch in
  etc/controlDict

      // Style for "ExecutionTime = " output
      // - 0 = seconds (with trailing 's')
      // - 1 = day-hh:mm:ss

   ExecutionTime = 112135.2 s  ClockTime = 113017 s

   ExecutionTime = 1-07:08:55.20  ClockTime = 1-07:23:37

- Callable via the new Time::printExecutionTime() method,
  which also helps to reduce clutter in the applications.
  Eg,

     runTime.printExecutionTime(Info);

  vs

     Info<< "ExecutionTime = " << runTime.elapsedCpuTime() << " s"
         << "  ClockTime = " << runTime.elapsedClockTime() << " s"
         << nl << endl;

--

ENH: return elapsedClockTime() and clockTimeIncrement as double

- previously returned as time_t, which is less portable.

- use succincter method names that more closely resemble dictionary
  and HashTable method names. This improves method name consistency
  between classes and also requires less typing effort:

    args.found(optName)        vs.  args.optionFound(optName)
    args.readIfPresent(..)     vs.  args.optionReadIfPresent(..)
    ...
    args.opt<scalar>(optName)  vs.  args.optionRead<scalar>(optName)
    args.read<scalar>(index)   vs.  args.argRead<scalar>(index)

- the older method names forms have been retained for code compatibility,
  but are now deprecated

Resolves bug-report https://bugs.openfoam.org/view.php?id=2511

Old:
- Previous versions created k and epsilon fields by default, and
  then processed omega and nuTilda fields if present.
- Depending on the choice of turbulence model, not all of these fields
  would be used, and could lead to errors when running some utilities
  due to erroneous values.
- If the omega field did not exist, it would be derived from the epsilon
  field, and also inherit the epsilon boundary conditions (wall
  functions)

New:
- This version will only update fields that already exist on file, i.e.
  will not generate any new fields, and will preserve the boundary
  conditions

The deprecated non-const tmp functionality is now on the compiler switch
NON_CONST_TMP which can be enabled by adding -DNON_CONST_TMP to EXE_INC
in the Make/options file.  However, it is recommended to upgrade all
code to the new safer tmp by using the '.ref()' member function rather
than the non-const '()' dereference operator when non-const access to
the temporary object is required.

Please report any problems on Mantis.

Henry G. Weller
CFD Direct.

Moved file path handling to regIOobject and made it type specific so
now every object can have its own rules. Examples:
- faceZones are now processor local (and don't search up anymore)
- timeStampMaster is now no longer hardcoded inside IOdictionary
  (e.g. uniformDimensionedFields support it as well)
- the distributedTriSurfaceMesh is properly processor-local; no need
  for fileModificationChecking manipulation.

ENH: applyBoundaryLayer - determine compressibility automatically by the presence of a thermophysicalProperties file

Avoids the clutter and maintenance effort associated with providing the
function signature string.

The old separate incompressible and compressible libraries have been removed.

Most of the commonly used RANS and LES models have been upgraded to the
new framework but there are a few missing which will be added over the
next few days, in particular the realizable k-epsilon model.  Some of
the less common incompressible RANS models have been introduced into the
new library instantiated for incompressible flow only.  If they prove to
be generally useful they can be templated for compressible and
multiphase application.

The Spalart-Allmaras DDES and IDDES models have been thoroughly
debugged, removing serious errors concerning the use of S rather than
Omega.

The compressible instances of the models have been augmented by a simple
backward-compatible eddyDiffusivity model for thermal transport based on
alphat and alphaEff.  This will be replaced with a separate run-time
selectable thermal transport model framework in a few weeks.

For simplicity and ease of maintenance and further development the
turbulent transport and wall modeling is based on nut/nuEff rather than
mut/muEff for compressible models so that all forms of turbulence models
can use the same wall-functions and other BCs.

All turbulence model selection made in the constant/turbulenceProperties
dictionary with RAS and LES as sub-dictionaries rather than in separate
files which added huge complexity for multiphase.

All tutorials have been updated so study the changes and update your own
cases by comparison with similar cases provided.

Sorry for the inconvenience in the break in backward-compatibility but
this update to the turbulence modeling is an essential step in the
future of OpenFOAM to allow more models to be added and maintained for a
wider range of cases and physics.  Over the next weeks and months more
turbulence models will be added of single and multiphase flow, more
additional sub-models and further development and testing of existing
models.  I hope this brings benefits to all OpenFOAM users.

Henry G. Weller

This reverts commit c5bea524.