During an interrupt handler, interrupts are implicitly disabled. They
will be re-enabled when the interrupt handler returns.
Due to some changes that were made, varous calls will re-enable
interrupts after they're finished. Examples of this include calling
`CALLBACK_CRITICAL_END` and getting the number of ticks with
`port_get_raw_ticks()`.
This patch prevents this from happening by doing two things:
1. Use standard calls in `port_get_raw_ticks()` to disable and re-enable
interrupts, preventing nesting issues, and
2. Increase the nesting count inside `isr()`, reflecting the implicit
call that is made by hardware when an interrupt is handled
This helps to address #3841.
Signed-off-by: Sean Cross <sean@xobs.io>