How do I create .hex or .flash files in IDE?

The application Makefile has a 'mem_init_install' target that uses the BSP mem_init.mk.

Here is the help target from a Nios II application project Makefile for reference

help :

@$(ECHO) "Summary of Makefile targets"

@$(ECHO) " Build targets:"

@$(ECHO) " all (default) - Application and all libraries (including BSP)"

@$(ECHO) " bsp - Just the BSP"

@$(ECHO) " libs - All libraries (including BSP)"

@$(ECHO) " flash - All flash files"

@$(ECHO) " mem_init_generate - All memory initialization files"

@$(ECHO) " mem_init_install - All memory initialization files (copy files to Quartus II project)"

@$(ECHO) " Clean targets:"

@$(ECHO) " clean_all - Application and all libraries (including BSP)"

@$(ECHO) " clean - Just the application"

@$(ECHO) " clean_bsp - Just the BSP"

@$(ECHO) " clean_libs - All libraries (including BSP)"

@$(ECHO) " Run targets:"

@$(ECHO) " download-elf - Download and run your elf executable"

@$(ECHO) " program-flash - Program flash contents to the board"