fix various including problem

1: replace quote includes with bracket includes
2: add missing kernel autoconf
3: remove one unused include

sel4runtime: include configs

since global autoconf is removed, we need to manually add
back the kernel config and sel4runtime_Config

Update licence dates.

Change __thread to __stack and use correct initial value.

Change the identifiers to refer to the stack instead of the thread and
use the top (for a descending stack) on all platforms.

Move crt files to separate folder for separate build