doc: Use west everywhere to build and flash

Instead of having a mix of west and CMake/ninja instructions for
building and flashing, document it using only west. This will help
clarify that west is the default build tool in Zephyr and should also
reduce confusion over what tool to use.
Note that the biggest change is changing the default in
doc/extensions/zephyr/application.py for :tool:, from all to west.

Signed-off-by: Carles Cufi <carles.cufi@nordicsemi.no>