This is done through the SAV command, where you can specify any or all of the files & directories in the IFS, even including the native file system of IBM i. Note that in the native file system, you do have to specify the objects & directories you want using their path names and object types. But if you’ve already saved those objects using the native save commands (SAVOBJ, SAVLIB, etc.), then you can specify in the SAV command to omit them.
Here’s a basic example of how you’d save the entire IFS except for the native file & library system, which would typically be done through the regular save commands and thus could be omitted here.
OBJ( (‘/*’) (‘/QSYS.LIB” *OMIT)
That’s a variation that saves /home/MYHOME into a savefile in QGPL named MYSAVF. The default for the directory subtree parameter on the SAV command is SUBTREE(*ALL), so everything within /home/MYHOME is also saved.