doc: Relocate and revise "Application Fundamentals" material

Relocates material that outlines the structure of a Zephyr application
so that it appears at the beginning of the "Application Development
Primer". (i.e. The primer now tells the reader the file structure of
an application, then explains how to create these files.)

Revises the description of the MDEF file to make it a bulleted item
(like the other file types are) and improve readability.

Change-Id: I9f003b8317257c927bea752da55cc434f957592c
Signed-off-by: Allan Stephens <allan.stephens@windriver.com>