The SAP SW Chain Job stores Chain ID in agent install directory.
Why does the SAP BW Chain job create and write to <agent_install_dir>/Root/<manager>?
CA WA Agent for SAP
The SAP SW Chain Job has "SourceDir" setting. This variable keeps the path of Root directory. The directory is used to write any Chain ID the agent receives. The directory setting is not configurable and always points to <agent_install_dir>/Root/<Manager>/MAIN.
This is normal behaviour for the CA WA SAP Agent.
Note: The <agent_install_dir>/Root folder will require a cleanup. These files are not cleaned as part of spool cleanup. Users may write a script to clean these files or do a manual cleanup.