The following are stored in submodules:
submodules/binutils-gdb/
submodules/buildroot/
submodules/gcc/
submodules/glibc/
submodules/linux/
submodules/qemu/
So you can modify source, rebuild and that's it, its in the VM.
E.g., let's hack the linux kernel:
asmlinkage __visible void __init __no_sanitize_address start_kernel(void)
{
pr_info("I'VE HACKED THE LINUX KERNEL!!!");
Rebuild Linux:
./build-linux
Rerun:
./run
And after boot we see:
<6>[ 0.000000] I'VE HACKED THE LINUX KERNEL!!!