Fixed errors reported on IBM XL compiler, as well as handling of CUDA/OPENCL-specific code, and many warnings.

Reorganization of some of the tests into the examples directory. Updates to some examples, notably yalaplace, which is now better documented and has better features.

Converted #include lines to use qualified names for public headers. However, this is not enforced at the moment in the build system.

Added CMake build system files
Added mesh demos, tests and associated data
Added tinyxml library in contrib
Added log library and sorted_array.h in src/common
Modified .gitignore to ignore backup files and build products