Mojo shell on Android: organise initializations.

This patch moves application-level initializations that don't depend on
the intent parameters to MojoShellApplication, leaving MojoShellActivity
as a handler for incoming intents.

Also, this documents a gotcha related to Activity vs Application
lifecycle in a comment.

BUG=None
R=qsr@chromium.org

Review URL: https://codereview.chromium.org/781483002