- The value from -outputThreshold was used in the code,
  but the option definition itself was somehow missed.

- polyMesh constructor from cell shapes invoked 'removeFiles'.
  This may or may not be what the caller wants or expects.
  With the ParaView blockMesh viewer, this behaviour causes deletion of
  all mesh data (points, faces, etc) when the viewer is refreshed.

  Triggered even when just building the blockMesh topology.

- only a few places that construct a polyMesh from cell shapes
  (mostly mesh conversion utilities).
  Ensure that the file removal (if any) occurs in the application
  and *not* as a side-effect of calling the polyMesh constructor.

--

  blockMesh (application)
    - The placement of the removeFiles seems to also remove freshly
      generated sets (Bug or feature to remove sets?)

  +-----------------------+---------------+------------------+
  | Application           | Constructor   | removeFiles      |
  |                       | (patch info)  | new / existing   |
  +-----------------------+---------------+------------------+
  | blockMesh             | dictionary    | existing         |
  | ansysToFoam           | names         | new              |
  | cfx4ToFoam            | dictionary    | new              |
  | fluentMeshToFoam      | names         | new              |
  | gambitToFoam          | dictionary    | new              |
  | gmshToFoam            | names         | new              |
  | ideasUnvToFoam        | names         | new              |
  | kivaToFoam            | dictionary    | new              |
  | mshToFoam             | names         | new              |
  | netgenNeutralToFoam   | names         | new              |
  | plot3dToFoam          | names         | new              |
  | tetgenToFoam          | names         | new              |
  | vtkUnstructuredToFoam | names         | new              |
  +-----------------------+---------------+------------------+

This is part of #340.

Resolves bug-report http://bugs.openfoam.org/view.php?id=2372

Resolves bug-report http://bugs.openfoam.org/view.php?id=2374

Resolves bug-report http://bugs.openfoam.org/view.php?id=2366

- Recursive searching for objects within a registry is now optional
  (previous it was always done).

  A recursive search effectively blocks the construction of sub-sub-registries
  if their names are 'masked' by some parent level sub-registry with
  the same name! (BUG)

- Recursive search is now turned OFF by default, which makes it consistent
  with dictionary and probably causes the least number of surprises.

----
Various new convenience methods added:

lookupObjectRef()
- returns a non-const reference.
  For example,

      volScalarField& U = mesh().lookupObjectRef<volScalarField>("U");

  Instead of

      volScalarField& U = const_cast<volScalarField&>
      (
          mesh().lookupObject<volScalarField>("U")
      );

--
lookupObjectPtr()
- returns a const pointer, and nullptr on failure.
  For example,

      const volScalarField* Uptr = mesh().lookupObjectPtr<volScalarField>("U");
      if (Uptr)
      {
          const volScalarField& U = *Uptr;
          ...
      }

  Instead of

      if (mesh().foundObject<volScalarField>("U"))
      {
          const volScalarField& U = mesh().lookupObject<volScalarField>("U");
          ...
      }

--
lookupObjectRefPtr()
- returns a non-const pointer, and nullptr on failure.
  For example,

      volScalarField* Uptr = mesh().lookupObjectRefPtr<volScalarField>("U");
      if (Uptr)
      {
          volScalarField& U = *Uptr;  // use as reference
          (*Uptr) = ...;              // or use directly
      }

  Instead of

      if (mesh().foundObject<volScalarField>("U"))
      {
          volScalarField& U = const_cast<volScalarField&>
          (
              mesh().lookupObject<volScalarField>("U")
          );
      }

--
sortedNames()
- now works with template parameters and with regular expression
  matching as well.
  For example,

      wordList names  = mesh().sortedNames();
      wordList fields = mesh().sortedName<volScalarField>();

  Instead of

      wordList names  = mesh().sortedNames();
      wordList fields = mesh().names<volScalarField>();
      Foam::sort(fields);

--

- test clearly shows failure to insert a sub-registry when it has
  the same name as one of the parent sub-registry.

- the user might otherwise be unaware of the changed location

- vtkkwiml headers use old-style casts, so reduce compile-time warnings

  - provides support for manipulating polyMesh/boundary

  - changed behaviour of disableFunctionEntries option to preserve
    #include

  - dictionary: added reading of lists of dictionaries.
    + each list element may be accessed using the 'entryDDD' keyword
      according to their list index.

Patch contributed by Mattijs Janssens

- these directories are sometimes used for a central, non-thirdparty, non-system
  installation

- leave gmp and mpfr as is, since it is not clear how these would interact with system
  versions

cellZones and pointZones can now be created in one action without the
need to first create a cellSet or pointSet and converting that to the
corresponding zone, e.g.

actions
(
    // Example: create cellZone from a box region
    {
        name    c0;
        type    cellZoneSet;
        action  new;
        source  boxToCell;
        sourceInfo
        {
            box   (0.04 0 0)(0.06 100 100);
        }
    }
);

- identical code was present in surfaceCheck (original source),
  and isoSurface, isoSurfaceCell (copies).

- add in a MeshedSurface<face> variant as well, since this will likely
  be needed in the near future

- The null constructor already creates a dimensionless Zero,
  but named "undefined".

  Provide an constructor for a dimensioned Zero,
  but named "0" for universal clarity to its value.

- only occurs in combination with distributedTriSurfaceMesh in snappy.

- workaround similar to that previously used for surfaceRedistributePar
  (issue #60).

Minor adjustment of incompressible motorBike tutorial to detect use of
distributedTriSurfaceMesh.

- there was a slight mix of MUST_READ and MUST_READ_IF_MODIFIED
  but with no obvious code to handle runtime modified values
  of the decomposition, or how this works with alternative
  dictionaries.