Most robust approach is to replace nested loops with BOUT_FOR loops as
this defers the zp/zm offsetting to the SpecificInd code

…ng bracket code

Doesn't use global `mesh`, instead uses `Field::getMesh()`, and constructs return
fields using this `localmesh`.

Loops in Z use `zstart`/`zend`, or changed to use `BOUT_FOR`

Updating the cxx file functions to use these new features.

* next: (1066 commits)
  Fix more typos in BoutMesh boundary Region y-ranges
  Add implementation of Field2D::applyBoundary(BoutReal time)
  Fix typos in BoutMesh boundary Region y-ranges
  Fixes for FV::Div_a_Laplace_perp
  Add Options::withDefault(Options&) to manual
  Set y-direction of FieldPerp results in ParallelTransformIdentity
  Do not calculate parallel slices for field-aligned fields
  Allow default value of Options to be set from another Options object
  Unit test ParallelTransformIdentity::toFieldAligned/fromFieldAligned
  Set y-direction of results in ParallelTransformIdentity
  Correct Field3D->FieldPerp in error message
  RGN_NOBNDRY in FieldPerp unit tests toFieldAligned and fromFieldAligned
  Unit tests for FieldPerp toFieldAligned and fromFieldAligned
  Add support for shifting a FieldPerp toFieldAligned/fromFieldAligned
  More tests for case sensitivity/insensitivity in options unit tests
  Convert Options::isSection() argument to lower case
  Update required Jinja2 version to avoid CVE-2019-10906
  Move Gridfile::get implementations for Field3D/Field2D to .cxx
  typo
  Warn about random failures in test
  ...

* next: (26 commits)
  Make manual entry on file I/O for FieldPerps clearer
  Rename safeAtReverse to safeAt
  Use BoutComm::rank() in datafile.cxx
  Add FieldPerp to File I/O documentation
  Throw in unimplemented 'int' version of GridFromOptions::get
  Make sure yindex_global is invalid in DataFormat::writeFieldAttributes
  HDF5 version of I/O test with reading from restart files
  I/O test with reading from restart files
  Make restart.redistribute work for FieldPerps
  Add FieldPerp to test-io and test-io_hdf5
  More FieldPerp support in datafile.py
  Add FieldPerp support to collect.py
  Loading FieldPerp from grid, only communicate and checkData if valid
  Don't allocate in Mesh::get
  GridFromFile: only allocate FieldPerp when actually reading
  Read attributes when getting Fields from grid-file
  Add FieldPerp version of Mesh::get()
  Implement FieldPerp capability in FieldFactory
  Don't use DataFormat::mesh when it might be nullptr
  Move readFieldAttributes/writeFieldAttributes to DataFormat
  ...

* next: (80 commits)
  Deprecate Karniadakis solver
  Remove Laplace3D
  Don't specify boundary regions in D2DXDY
  Use function_traits<T>::arg_t<N> in SUNDIALS wrappers
  Add some tests for function_traits
  Provide function_traits<T>::arg_t<0> for ease of use
  Remove autoconf macros for handling SUNDIALS integer types
  Replace SUNDIALS int types with `function_traits` or sunindextype
  Add traits class to get types of function arguments
  fix nc-format
  Manual section on mixed second derivatives
  In D2DXDY take y-derivative first, apply boundary condition before DDX
  Take z-derivative before x-derivative in D2DXDZ
  Simplify location-setting in D2DYDZ
  Handle attributes for missing variables
  Revert "Hypnotoad: 'H' is derivative of integral"
  Default initialise member variables
  Fix return type on empty Petsc Laplace solve
  Add LaplacianNaulin::resetMeanIterations
  Replace old-style C casts with static_cast in PetscSolver
  ...