By compiling your RPG/400 programs and CL programs with the right parameters you can use the ILE source level debugger...
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on these objects as well as RPGLE and CLLE objects.
For RPG, set the OPTION parameter of CRTRPGPGM to *LSTDBG or *SRCDBG. (*LSTDBG is better because it will include any /COPY source in the debug view.) For CL, set the OPTION parameter of CRTCLPGM to *SRCDBG. Then when you STRDBG for the program make sure you set the OPMSRC parameter to *YES.
I've set up PDM options to do the compiles with the correct parameter selections, and I created a simple CL program and command that does the correct STRDBG based on the attribute of the program.�The CL does a RTVOBJA on the program, and if the object is RPGLE or CLLE it does a simple STRDBG; otherwise it does the STRDBG with OPMSRC(*YES).