doc: application: clean up overview

A few things are stale or missing:

- Using the term 'kernel' is outdated at this point. It's been years
  since Zephyr was just a kernel, and we now include many modules as
  well as our internal subsystems and driver layers. Make that clearer
  in the overview.

- Devicetree overlays are a basic piece of zephyr applications and
  they're worth highlighting at this introductory place as well. Note
  that neither app.overlay or prj.conf are actually required to be
  present, so if we're mentioning prj.conf here, we might as well
  mention app.overlay too.

- Explain the basic purpose of and differences between Kconfig
  fragments and DT overlays.

Clean up some other language and provide some more cross references.

Signed-off-by: Marti Bolivar <marti.bolivar@nordicsemi.no>