Changing the physical layout of the code (include and src) and adding inline

namespaces to reflect the physical layout logically.

Change log:
namespace and folder are interchangable in the following:
* 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 detailed 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 object 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:
    - Create 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