doc: Clarify application configuration

The current application configuration documentation makes it a bit
unclear that configuration files are merged. Rewrite the documentation
to explicitly talk about merging, which I think is less confusing.

Remove the following section from the introduction as well, as I think
it might make people wonder how they can have an existing kernel
configuration when they haven't created one. The updated configuration
section (which the introduction now has a forward reference to)
clarifies the zephyr/.config bit anyway.

    If omitted, the application's existing kernel configuration option
    values are used; if no existing values are provided, the kernel's
    default configuration values are used.

Signed-off-by: Ulf Magnusson <ulfalizer@gmail.com>