Change the file and folder layout, adding inline namespaces so the logical
namespaces match the physical locations of the files.
This also improves the organization and presentation of Doxygen documentation.

Change log:
* general:
    - Change names of classes and files to Snake case, starting with a capital
      letter
    - Tidy documentation and add @briefs everywhere
    - Adding namespaces inside #ifdef __cplusplus pragmas to C-files, such that
      the members will appear at the correct location in the documentation
* flow:
    - Move most of the classes in the flow namespace to a detail namespace
* piol:
    - Move communicator to utils namespace and rename CommunicatorInterface.hh
      to just Communicator.hh
    - Move Read and Write classes to namespace file and rename to Input_file and
      Output_file
    - Move Object read/Write-classes to detail namespace inside namespace file
    - Move ExSeis[PIOL] to configuration namespace
    - Rename Binary_file to IO_driver and move to own namespace
    - Create metadata namespace with Trace_metadata_key (formerly Meta) and a
      rules namespace containing everything concerning the rules for SEGY files
    - Create namespace segy for utilities and Trace header offsets (formerly Tr)
    - Create sort namespace inside operations namespace for the sort operations
* utils:
    - Move Distributed_vector classes to namespace of the same name
    - Remove mpi namespace and create mpi_utils for utilities and move
      MPI_Distributed_vector to distributed_vector namespace and MPI_types to
      types namespace
    - Create types namespace for various kinds of type definitions

Change log:
* Add details of requirements for building on macOS

Change Log:
* Add flush method to WriteSEGY class
* Fix minor typos in docs
* Add additional output method to Set class
* Add clean and free methods for MPI_Binary_file and
MPI_Binary_file::Opt classes
* Add clang-tidy modernize-redundant-void-arg and fix issues

Change Log:
* CMake dependency bumped to 3.10.
* Moved to target-oriented CMake set-up.
* ExSeisDat can be included in a project via add_subdirectory.
* Compiled/installed ExSeisDat can be used with find_package from the
  ExSeisDat build directory or install directory.
* FFTW3 and MPI now linked as imported targets.
* Added options to enable/disable specific tests
* Added CMake option to add development flags used by the CI environment
  for GCC and Clang.

Change Log:
* Added documentation to special member functions.
* Fixed configure_file removing `=` after `@INCLUDE` in Doxyfile-man.
* Added ignoring `detail` namespaces in Doxygen.
* Moved a number of classes into the `detail` namespace.

Change Log:
* CI for clang-format uses Ubuntu 19.04 and clang-format-8 package.
* Updated .clang-format for clang-format 8.
* Changed line continuation indent to 4 spaces.

Change Log:
* Added exseis-metadata-converter utility program for extracting SEG-Y
  metadata out to a CSV file.
* Added dependency on CLI11 for argument parsing.
* Added CLI11 to third_party directory.
* Changed Binary_file buffer signature from `unsigned char*` to `void*`.
* Added manpage generation to Doxygen configurations.

Change log:
* Removed muting from taper function, as the functionality is now included in operation mute.

Change log:
* Added continuous integration
  * Formatting, documentation, static analysis
  * Compilation and testing with GCC and Clang on Linux with FFTW3 and MPICH.
* Refactored trace metadata storage classes. Now called `Trace_metadata`.
* Refactored low-level I/O class, now called `Binary_file`, with an MPI implementation called `MPI_Binary_file`.
* Refactored file reader and writer interfaces, removing the need for an object layer, making specialization for new seismic file types more obvious.
* Renamed namespaces to use all lower-case.
* Added a number of static analysis checks, including the cases of variables and functions.

Redo naming and structure S-01696

See merge request oilgas/ExSeisDat!5

IBM to IEEE conversion D-01132

See merge request oilgas/ExSeisDat!4

Moved AGC and taper into utils/signal_processing. Split taper.hh into taper.h and Taper_function.h. Replaced enum lookup for taper functions with directly exporting function pointers. Fixed minor bug with application of the right taper. Changed docs for signal_processing to group AGC and taper, and have gain functions and taper functions in separate groups.

Added clang-tidy flags: readability-redundant-string-init, readability-container-size-empty, readability-implicit-bool-conversion.

Added readability-avoid-const-params-in-decls clang-tidy flag. Changed MPI, FFTW and googletest includes to system includes in CMakeLists.txt and test/CMakeLists.txt.

Added gain_control, number_encoding, and decomposition inline namespaces to exseis::utils. Added some C API grouping to those namespaces.

Changed interfaces for number conversion to be more clear what type of data is coming in and out, so a programmer must be more explicit about what is native data and what are non-native bytes.

Replaced getBigEndian with to_big_endian. Now returns big-endian bytes rather than setting them in-place. WIP.

Removed utils/constants.hh. Moved or removed unnecessary typedefs in utils/typedefs.h. Renamed llint, geom_t, and trace_t to Integer, Floating_point, and Trace_value.

Put utils, PIOL, and Flow libraries into exseis::utils, exseis::PIOL, and exseis::Flow namespaces respectively. Moved some files into utils that were needed by other utils, and removed PIOL dependencies.

Removed printError from mpi_utils.hh, removing dependency on the Logger. Added MPI_error_to_string function instead and replaced instances of printError in the codebase with equivalent call to the logger and MPI_error_to_string. Split the functions out and into utils/mpi directory. Placed the functions under an exseis::utils namespace.

Added include/ExSeisDat/utils directory for utilities that aren't PIOL of Flow specific. Moved PIOL/operations/agc.h to utils/gain_control/AGC.h. Removed the AGCType enumeration in favour of function pointers to the gain functions. Moved gain functions to utils/gain_control/Gain_functions.h, adding the Gain_function type for the function pointers. Refactored src/agc.cc, splitting it into src/utils/gain_control/AGC.cc and src/utils/gain_control/Gain_function.cc. Added a documentation line for the PIOL namespace, allowing functions to appear in the doxygen documentation.

Removed repetitive appending of executables to lists in examples/CMakeLists.txt and utils/CMakeLists.txt.

Renamed Decomposed_range to Contiguous_decomposition. Renamed decompose_range to block_decompose. Renamed decomposed_index_location to block_decomposed_location. Removed util/sglobal.h, util/sglobal.c, util/ctest.h, and util/ctest.c.

Added assertion that types used for MPI_Distributed_vector are trivially copyable to ensure bitwise copy across MPI processes works as expected. Replaced the tuple used for gathers with a struct called Gather_info, which is trivially copyable.

Redesigned Distributed_vector, pulling the MPI out into a MPI_Distributed_vector implementation. Renamed decompose to decompose_range, along with renaming a number of parameters and classes in decompose.h.

Pulled running clang-tidy from scripts/run_linter.sh to scripts/lint.sh. Renamedrun_linter.sh to run_lint.sh. Renamed run_clang_format.sh to run_format.sh. Added argument to pass build directory to run_lint.sh. Added scanning .c files in run_lint.sh.