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doxygen updates for code files involved in I/O and initialization #775

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Job	Run time
setup	16s
build (Ifremer1)	1m 17s
build (NCEP_st2)	1m 14s
build (NCEP_st4)	1m 16s
build (ite_pdlib)	1m 27s
build (NCEP_st4sbs)	1m 16s
build (NCEP_glwu)	1m 31s
build (OASACM)	1m 22s
build (UKMO)	1m 25s
build (MULTI_ESMF)	1m 15s
	12m 19s