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Changes to setup and initdir for nested domains NEA9 and ARCT18 #173

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Job	Run time
setup	51m 41s
build (Ifremer1)	1m 41s
build (NCEP_st2)	1m 23s
build (NCEP_st4)	1m 26s
build (ite_pdlib)	1m 41s
build (NCEP_st4sbs)	1m 27s
build (NCEP_glwu)	1m 27s
build (OASACM)	1m 32s
build (UKMO)	1m 20s
build (MULTI_ESMF)	1m 17s
build (FCOO)	1m 27s
	1h 6m 22s