A system program is a generic program provided by the underlying operating system and used in unmodified form in the legacy application: a mainframe sort utility, for example. You need to identify system programs to the parser so that it can distinguish them from application programs and create relationships for them with their referencing files.
The most convenient way to identify the system programs your application uses is to run an unresolved report after verification. Once you learn from the report which system programs are referenced, you can identify them in the System Programs tab of the Workspace Options window and reverify any one of their referencing source files.