This boot files can be used for Application Development. It includes the FSBL and the PL configuration but no application. Handoff at the end of the booting stage is to JTAG.
This image file can be loaded into the QSPI flash, see https://deepjava.org/firstexample/boot_loader.
This boot files can be used for Deploying. It includes the FSBL and the PL configuration together with the hello world application. Handoff at the end of the booting stage is to this application.
BOOTflink2App.mcs will be used when creating a deep application which is loaded into the QSPI flash for deployment, see https://deepjava.org/firstexample/first_example_microzed_deploy. When deploying for the SD card, BOOTflink2App.bin is used. Launching the deep compiler will in both cases replace the existing hello world application with your deep image.