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Set volume to homogeneous index 0 and set boundaries to increasing
indices

* Update 'test-grid-creation': Check for correct boundary segmentation
* Add boundary segmentation datasets
* Add boundary segments to GMSH mesh files
* Update .mini files with new keys

* rename `grid.mappingFile` to `grid.mapping.file`.
* rename `grid.mappingFileDataset` to `grid.mapping.volume`.
* remove `grid.globalIndex`. Same functionality is provided by setting
    `grid.mapping.volume` to an integer index.
* add keys for boundary mapping datasets.

* Add nested class GridMapper::Boundary for helper functions regarding
    boundary side identification and handling
* Rewrite indexing functions of GridMapper<Grid, rectangular> to also
    work with lower-dim arrays

* Add function 'is_none' for checking if user input is 'none'
* Move functions 'to_lower' and 'get_grid_extensions' to new header

* Add module for grid creation
* Add author and date information
* Improve docstrings of classes and functions

Also, fix header in transport.hh

* GridMapper is now called internally by the constructor of GridCreator.
    The object is not returned by the creator anymore.
* Specialize GridMappers for 'gmsh' and 'rectangular' grids and
    derive them from GridMapperBase
* GridMapper now reads the mapping H5 file
* The grid is now retrieved from GridCreator
* Local element and boundary index maps are now retrieved from
    GridCreator
* Adapt simulations to expect GridCreator as argument

Minor changes:
* Store file name in H5File
* Add free function for lowercasing strings
* Add logger to GridMapper

Resolve "Add a logging framework for command line output"

Closes #92

See merge request !106

[ci skip]

* default logger for scaling is Richards
* pass logger to scaling adapters
* default logger for interpolators is base
* only InterpolatorFactory uses logger

Do not display the exception as 'error' message again

Rename groups.dox files to modules.dox

See merge request !118

* Adapt tests to use new initialization functions

* 'inifilename' is no longer available
* CalculationController does not take MPIHelper as argument anymore

Compiler complained about unused variables. Use the variable by
discarding it.

The argument will default to retrieving the base logger

Resolve "Add scaling field input"

Closes #18 and #110

See merge request !110

Includes information on how to initialize a program conveniently.
Add namespace Setup to it.

* 'Dorie::Setup::init' creates the ParameterTree, the base logger,
    and the MPIHelper and returns them as a tuple
* 'Dorie::Setup::debug_hook' halts the program for attaching a
    debugger
* Adapt executables to new functions
* Rename `common/setup_inifile.hh` to `common/setup.hh`
* Convert indentation to spaces in `common/setup.hh`

* Introduce global names for loggers and use them for retrieval
* Remove config file keys 'verbose' and fix values for 'logLevel'
* Add new functions for creating and retrieving loggers, even without
    MPIHelper (for critial messages)
* Create base loggers in 'main' functions of applications and tests

* Add formulae for functions implemented
* Add doxygen subgroups Parameterization and Interpolators
* Add author and date information

Evaluation of parameterizations must occur on leaf grid view then.