I’m not quite sure which debugger the iSeries System Debug Manager is – is it the one through the emulation screens (STRDBG command), or the WDSC debugger, RDi, or something completely different?
Your menu system is probably storing the library list in a file or data area, and reading it when a user goes into the menu system in order to set their session with that library list.
So you should be able to trace down the location where it stores that library list. You could read that file or data area in a CL program and then change the library list accordingly. Depending on how the library names are stored, whether they’re in separate records or one long field, you may need to build a string of all those names and then use that for the LIBL keyword of the CHGLIBL command. I recommend creating a command for that CL program, so that you could then just run the command to set your library list. The advantage of that is that if your library list ever has to be adjusted, you wouldn’t have to change your CL program, since it would get the library list from the same location as your menu system.
You would then just run your new command before starting your program(s) you wish to debug, or have your debugging tool run that command automatically when you start a debug session.