- convenient when bootstrapping some systems

- local token shifting was missing when getting the next file chunk
  (while in the middle of parsing that text).

  As well as adding the correct shifting, also tag the local buffer
  with nullptr when it is done. Be extra paranoid and check the
  raw buffer range before passing off to std::string.

Previously the coordinate system functionality was split between
coordinateSystem and coordinateRotation. The coordinateRotation stored
the rotation tensor and handled all tensor transformations.

The functionality has now been revised and consolidated into the
coordinateSystem classes. The sole purpose of coordinateRotation
is now just to provide a selectable mechanism of how to define the
rotation tensor (eg, axis-angle, euler angles, local axes) for user
input, but after providing the appropriate rotation tensor it has
no further influence on the transformations.

--

The coordinateSystem class now contains an origin and a base rotation
tensor directly and various transformation methods.

  - The origin represents the "shift" for a local coordinate system.

  - The base rotation tensor represents the "tilt" or orientation
    of the local coordinate system in general (eg, for mapping
    positions), but may require position-dependent tensors when
    transforming vectors and tensors.

For some coordinate systems (currently the cylindrical coordinate system),
the rotation tensor required for rotating a vector or tensor is
position-dependent.

The new coordinateSystem and its derivates (cartesian, cylindrical,
indirect) now provide a uniform() method to define if the rotation
tensor is position dependent/independent.

The coordinateSystem transform and invTransform methods are now
available in two-parameter forms for obtaining position-dependent
rotation tensors. Eg,

      ... = cs.transform(globalPt, someVector);

In some cases it can be useful to use query uniform() to avoid
storage of redundant values.

      if (cs.uniform())
      {
          vector xx = cs.transform(someVector);
      }
      else
      {
          List<vector> xx = cs.transform(manyPoints, someVector);
      }

Support transform/invTransform for common data types:
   (scalar, vector, sphericalTensor, symmTensor, tensor).

====================
  Breaking Changes
====================

- These changes to coordinate systems and rotations may represent
  a breaking change for existing user coding.

- Relocating the rotation tensor into coordinateSystem itself means
  that the coordinate system 'R()' method now returns the rotation
  directly instead of the coordinateRotation. The method name 'R()'
  was chosen for consistency with other low-level entities (eg,
  quaternion).

  The following changes will be needed in coding:

      Old:  tensor rot = cs.R().R();
      New:  tensor rot = cs.R();

      Old:  cs.R().transform(...);
      New:  cs.transform(...);

  Accessing the runTime selectable coordinateRotation
  has moved to the rotation() method:

      Old:  Info<< "Rotation input: " << cs.R() << nl;
      New:  Info<< "Rotation input: " << cs.rotation() << nl;

- Naming consistency changes may also cause code to break.

      Old:  transformVector()
      New:  transformPrincipal()

  The old method name transformTensor() now simply becomes transform().

====================
  New methods
====================

For operations requiring caching of the coordinate rotations, the
'R()' method can be used with multiple input points:

       tensorField rots(cs.R(somePoints));

   and later

       Foam::transformList(rots, someVectors);

The rotation() method can also be used to change the rotation tensor
via a new coordinateRotation definition (issue #879).

The new methods transformPoint/invTransformPoint provide
transformations with an origin offset using Cartesian for both local
and global points. These can be used to determine the local position
based on the origin/rotation without interpreting it as a r-theta-z
value, for example.

================
  Input format
================

- Streamline dictionary input requirements

  * The default type is cartesian.
  * The default rotation type is the commonly used axes rotation
    specification (with e1/e2/3), which is assumed if the 'rotation'
    sub-dictionary does not exist.

    Example,

    Compact specification:

        coordinateSystem
        {
            origin  (0 0 0);
            e2      (0 1 0);
            e3      (0.5 0 0.866025);
        }

    Full specification (also accepts the longer 'coordinateRotation'
    sub-dictionary name):

        coordinateSystem
        {
            type    cartesian;
            origin  (0 0 0);

            rotation
            {
                type    axes;
                e2      (0 1 0);
                e3      (0.5 0 0.866025);
            }
        }

   This simplifies the input for many cases.

- Additional rotation specification 'none' (an identity rotation):

      coordinateSystem
      {
          origin  (0 0 0);
          rotation { type none; }
      }

- Additional rotation specification 'axisAngle', which is similar
  to the -rotate-angle option for transforming points (issue #660).
  For some cases this can be more intuitive.

  For example,

      rotation
      {
          type    axisAngle;
          axis    (0 1 0);
          angle   30;
      }
  vs.
      rotation
      {
          type    axes;
          e2      (0 1 0);
          e3      (0.5 0 0.866025);
      }

- shorter names (or older longer names) for the coordinate rotation
  specification.

     euler         EulerRotation
     starcd        STARCDRotation
     axes          axesRotation

================
  Coding Style
================
- use Foam::coordSystem namespace for categories of coordinate systems
  (cartesian, cylindrical, indirect). This reduces potential name
  clashes and makes a clearer declaration. Eg,

      coordSystem::cartesian csys_;

  The older names (eg, cartesianCS, etc) remain available via typedefs.

- added coordinateRotations namespace for better organization and
  reduce potential name clashes.

- for installations with central (non-ThirdParty) location for KAHIP
  (eg, spack, EasyBuild)

- avoids compiler ambiguity when virtual methods such as
  IOdictionary::read() exist.

- the method was introduced in 1806, and was thus not yet widely used

- ignore implicit-fallthrough for ragel generated code.

- add -Wno-deprecated-declarations for c++LESSWARN.
  These principally associated with older CGAL versions and their use
  of particular mpfr routines.

- since 1612, FOAM_INST_DIR and foamInstDir longer have any
  special meanings when sourcing the bashrc or cshrc files.
  Thus no need for special treatment in any of the dispatch wrappers.

  Retained FOAM_INST_DIR as (unexported) variable in etc/bashrc,
  just in case people are using patched versions of etc/bashrc
  as part of their installation.

ENH: relax prefix restrictions on foamCreateVideo (issue #904)

- shift the implicit '.' to be part of the default prefix. This allows
  things like "-image myimages_00" to work as might be expected.

- this is consistent with compiler defaults, and helps Darwin users

- tie the MPI rules to the base compiler type *without* its version.
  Eg, linux64Gcc (which exists) instead of linux64Gcc81

- downgrades some diagnostics about nonconformant code from errors to
  warnings. Oddly enough, the errors actually arise from STL library
  elements shipped with gcc itself. Affects kahip compilation with
  gcc-6, gcc-7

- required if there is no system openmp and libomp or libgomp are
  only found in the clang hierarchy

STYLE: add some notes in the openmp rules.

- the _OPENMP macro is now used in low-level testing files

- allows enabling new warnings without causing messy output with older
  clang versions

- improvement documentation for surface sampling.

- can now specify alternative sampling scheme for obtaining the
  face values instead of just using the "cell" value. For example,

      sampleScheme    cellPoint;

  This can be useful for cases when the surface is close to a boundary
  cell and there are large gradients in the sampled field.

- distanceSurface now handles non-closed surfaces more robustly.
  Unknown regions (not inside or outside) are marked internally and
  excluded from consideration. This allows use of 'signed' surfaces
  where not previously possible.

- since PackedBoolList is now a compatibility typedef for bitSet,
  it is useful to have an additional means of distinction.

STYLE: simplify internal version tests and compiler defines.

- the API version is now conveyed via the OPENFOAM define directly.
  The older OPENFOAM_PLUS define is provided for existing code.

- parsing error state only arises from a missing final newline
  in the file (which the dnl macro does not capture).
  Report with a warning instead of modifying the dnl macro since
  we generally wish to know about this anyhow.

- add missing newline to YEqn.H file.

- handling of dead links (find -L -delete unsupported)

- remove ignore case flag on 's/../../i' used in have_scotch script.
  It is unneeded and not tolerated by Darwin's sed.

- avoid embedded comments in EXE_INC (Make/options files), which do
  not work well with the OSX LLVM cpp.
  It strips out the comments but also removes the continuation char.

STYLE: adjust notes about paraview library locations

- was somewhat redundant in wmake/rules/General/general anyhow

- generalize some of the library extensions (.so vs .dylib).
  Provide as wmake 'sysFunctions'

- added note about unsupported/incomplete system support

- centralize detection of ThirdParty packages into wmake/ subdirectory
  by providing a series of scripts in the spirit of GNU autoconfig.
  For example,

      have_boost, have_readline, have_scotch, ...

  Each of the `have_<package>` scripts will generally provide the
  following type of functions:

      have_<package>          # detection
      no_<package>            # reset
      echo_<package>          # echoing

  and the following type of variables:

      HAVE_<package>          # unset or 'true'
      <package>_ARCH_PATH     # root for <package>
      <package>_INC_DIR       # include directory for <package>
      <package>_LIB_DIR       # library directory for <package>

  This simplifies the calling scripts:

      if have_metis
      then
          wmake metisDecomp
      fi

  As well as reducing clutter in the corresponding Make/options:

      EXE_INC = \
          -I$(METIS_INC_DIR) \
          -I../decompositionMethods/lnInclude

      LIB_LIBS = \
          -L$(METIS_LIB_DIR) -lmetis

  Any additional modifications (platform-specific or for an external build
  system) can now be made centrally.

- permits platform-specific override of the general CGAL rules

- the previous grammar used

      '/*' { fgoto comment; }

  to start processing multi-line comments and

      comment := any* :>> '*/' @{ fgoto main; };

  as a finishing action to return to normal lexing, but seemed not to
  have been triggered properly.

  Now simply trap in a single rule:

      '/*' any* :>> '*/';             # Multi-line comment

STYLE: use more compact dnl (delete to newline)

  OLD:   [^\n]* '\n'
  NEW:   (any* -- '\n') '\n'

  eliminates the intermediate state

- adjusted grammar to be more precise

- However, the new ragel-based parser is much faster
  than the others, and does not cause 'too many open files' error
  that the flex-based parser does (issue #784).

  The timings (using src/sampling as being somewhat representative)

    $ wclean; wmakeLnInclude -u .; time wmake -s dep

        3.4s  wmkdepend (ragel) [now default]
        5.7s  wmkdep (flex)
        6.1s  cpp -M

- The makeDepend script is for testing purposes only, but could used as
  a hook for other dependency generation systems (eg, ninja).
  It simply wraps 'cpp -M' in a form that is calling compatible with
  wmkdepend.

BUG: wmkdepend parser was missing optional leading space on #include match

STYLE: use -G2 (goto-based) option for wmkdepend state machine

- the machine is compact with few states and lends itself to this

- a partial selection from https://github.com/mrklein/openfoam-os-x
  with adjustments. The primary purpose is to reduce header-level
  incompatibilities and to provide a common set of make rules to allow
  easier patching (or re-integration).

  This is similar to efforts (Feb 2010) but using ragel
  (https://en.wikipedia.org/wiki/Ragel) instead of the now defunct
  coco/r. The modified commit message from 2010:

ENH: add C++-based wmkdepend parser (uses ragel grammar).

- This avoids dependency on lex/flex and provides better encapsulation
  for buffer switching. As a result, the maximum number of open files
  only corresponds to the include depth.

--

Note that the flex source and rules are still available, but are not
deactivate (see wmake/rules/General/transform)

- less efficient and less portable than using single-pass processing

- easier to ensure that flags are consistent

- primary points for an external user are the polyMesh constructor

- add config info for gcc-7.3.0

COMP: intel-2017. Ignore unknown pragmas. Disambiguate method resolution.