added optional argument description (Fixes #347)

Optional argument listed.

@andy @mark Could you confirm/merge?

See merge request !90

- 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              |
  +-----------------------+---------------+------------------+

Surf field sampling

See merge request !87

ENH: runTimePostProcessing - added option to clear/remove objects after use

When specifying line and surface function-object-based visualisation, use the optional `clearObjects` flag to indicate that source objects should be removed/cleared after use.

Test case: [cavity.tgz](/uploads/62cc2761d132f42456f2af08f1499eba/cavity.tgz)

Syntax:

```
    surfaces
    {
        cuttingPlane1
        {
            type            functionObject;
            functionObject  cuttingPlane;
            clearObjects    yes;              // new option
            ...
```

Note: only files that have been used will be removed, e.g. if a function object has created multiple surface files, unused files will remain at the end of the run - in the attached case the p surface remains...

See merge request !89

- boost uses old-style casts for null and others

Integration of ihcantabria wave models

Integration of functionality produced by The Environmental Hydraulics Institute "IHCantabria" (http://www.ihcantabria.com/en/)

- Original code introduced in commit 95e9467e
- Restructured and updated by OpenCFD into a new `waveModels` library available to the interFoam family of solvers

Main source:
`$FOAM_SRC/waveModels`

Tutorials:
`$FOAM_TUTORIALS/multiphase/interFoam/waveExample*`

Capabilities include:
- Wave generation
- Solitary wave using Boussinesq theory
- Cnoidal wave theory
- StokesI, StokesII, StokesV wave theory
    
- Active wave absorption at the inflow/outflow boundaries based on shallow water theory

IHCantabria Authors:
- Javier Lopez Lara (jav.lopez@unican.es)
- Gabriel Barajas (barajasg@unican.es)
- Inigo Losada (losadai@unican.es)

See merge request !88

- the configuration settings can be used for the third-party build,
  but the configuration is not yet actively enabled in
  etc/bashrc, etc/cshrc

- now defaults to 'log.$WM_OPTIONS' (eg, log.linux64GccDPInt32Opt)
  for more clarity and fewer potential name clashes when building
  multiple versions.

- additional surface and surfaceAndDirection modes

- extend the sampling concept to include surfMeshes and surfFields
  for storage.

- Note the createOnRead switch in surfMeshSamplers can be desirable in
  some situations to force creation of the surface faces within the
  constructor.

- currently only 'none' or 'sqrt', which can be useful in combination
  with integrate or averaging functions.

  - fieldAverage
  - mag
  - magSqr
  - readFields
  - fieldsExpression (add, subtract)

- similar to functionality available for IOobjectList, objectRegistry

- was using the ids coming from the zones instead of the sorted order
  from ensightFaces, which led to a clash in the mesh point maps that
  were manifest as a jumbled order.

BUG: missing newlines in foamToEnsight nfaced/nsided ASCII output

- was correct for foamToEnsightParts, but not for foamToEnsight

--
* Many thanks to Justin Graupman for all of his testing,
  which has been a great help in isolating and fixing various issues.

ENH: reduce number of variables, simplify code

- Note: use boolList instead of scalarList for managing the face signs
  since its lazy evaluation can be convenient when sign information is
  not required.