ZZS, alt_sys_init is called from alt_main()
this in turn is called from ctr0.s, which is the initial bootloader.
after returning from alt_sys_init(), alt_main() calls main(), and your application starts.
fro the ide, do a search->file alt_main.c to locate the system file alt_main.
if you want to be really clever, you can put a copy of alt_sys_init and alt_main files in your local project directory, alter it to your needs, and it will override the system file found in the HAL. in this way you can customise the devices initialised at boot time
ashone