cmake: Use updated mcu-driver-hal

Update mcu-driver-hal reference to remove the deprecated
mcu-driver-bootstrap CMake target from dependencies.

- Use standalone mbed-atomic lib.
- Use standalone mbed-trace lib.
- Update examples and tests to use delay / wait functions available for
  each platform.

Signed-off-by: Filip Jagodzinski <filip.jagodzinski@arm.com>