CSDS Move the index files into the reader.

examples/HydroTests/SedovBlast_3D/sedov.yml

examples/main.c

src/Makefile.am

src/csds.c

src/csds.h

src/csds_history.c

src/csds_history.h

src/csds_io.c

src/csds_io.h

src/engine.c

src/engine.h

src/engine_config.c

src/engine_io.c

tools/read_index_file.py