miniWeather(modernization): build system, directory structure, clang-format, use of most recent YAKL

[janciesko]

This adds the following changes: Build system

• Treats all external libraries via cmake/modules
• Supports building with YAKL installation
• Adds cmake configure options for all flavors

Example: The following cmake build system invocation is supported.

cmake -DCMAKE_CXX_COMPILER=mpicxx -DPNETCDF_ROOT=$(PNETCDF_INSTALL_PATH) -DYAKL_ROOT=$(YAKL_INSTALL_PATH) DKokkos_ROOT=$(KOKKOS_INSTALL_PATH) -DMW_ENABLE_ALL=On

Directories:

• c -> cpp: Renaming in order to indicate the use of cpp files
• cpp->cpp_yakl: Renaming in order to indicate the use of cpp files and YAKL
• build->scripts: Renaming build directory to scripts in order to avoid confusion

Formatting:

• Adds script to apply clang-format

Code:

• Source files using YAKL were updates to not use the deprecated YAKL API but to use Kokkos instead.