In the green screen the following CL command works:
CRTLF FILE(CO99IN/INDEXTPU) SRCFILE(IT/DDSSRC) SRCMBR(INDEXTPU)

The library list contains (LibName, Type):
QSYS SYS
QSYS2 SYS
QHLPSYS SYS
QUSRSYS SYS
@SYS SYS
CO CUR
IT USR
CO99IN USR
QGPL USR
QTEMP USR

In my Java Program:
With JT400 I issue the following CL Commands:
ADDLIBLE LIB(CO)
ADDLIBLE LIB(IT)
ADDLIBLE LIB(CO99IN)
CRTLF FILE(CO99IN/INDEXTPU) SRCFILE(IT/DDSSRC) SRCMBR(INDEXTPU)

The CRTFL file immediately above now fails with:
Command CRTFL in library *LIBL not found.
Error found on CRTFL command.


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