Fixed remaining issues with proper CMake pipeline.

czi/source_code/CMakeLists.txt

czi/source_code/app/CMakeLists.txt

czi/source_code/app/include/bsdiff/api_bsdiff.h

czi/source_code/app/include/bsdiff/bsdiff.h

czi/source_code/app/include/bsdiff/bspatch.h

czi/source_code/app/include/cli/args.hxx

czi/source_code/app/include/compression/benchmark.h

czi/source_code/app/include/compression/compressors.h

czi/source_code/app/include/custom_types.h

czi/source_code/app/include/czi/czi_file.h

czi/source_code/app/include/czi/czi_parser.h

.../app/include/czi/czi_parts/attachment_directory_segment.h

...urce_code/app/include/czi/czi_parts/attachment_entry_a1.h

...ource_code/app/include/czi/czi_parts/attachment_segment.h

czi/source_code/app/include/czi/czi_parts/compression_type.h

czi/source_code/app/include/czi/czi_parts/dimension.h

...urce_code/app/include/czi/czi_parts/dimension_entry_dv1.h

...ource_code/app/include/czi/czi_parts/directory_entry_dv.h

...urce_code/app/include/czi/czi_parts/file_header_segment.h

czi/source_code/app/include/czi/czi_parts/metadata_segment.h