Logger: cleanup

logger/logger_header.c

logger/logger_header.h

logger/logger_index.c

logger/logger_index.h

logger/logger_loader_io.c

logger/logger_logfile.c

logger/logger_logfile.h

logger/logger_particle.c

logger/logger_particle.h

logger/logger_python_wrapper.c

logger/logger_reader.c

logger/logger_reader.h

logger/logger_time.c

logger/logger_time.h

logger/logger_tools.c

logger/tests/testLogfileHeader.c

logger/tests/testLogfileReader.c

src/engine.c

src/engine.h

src/logger.c