Consolidate configuration into a single config file

Simplifies and consolidates configuration into a single file, which
makes it easier to reason about for developers and work with for
deployment. Updates other code accordingly.

Changes secret keys so we now use a different SECRET_KEY (used by Flask
for signing cookies) for the source and document interfaces. This
exposes some interesting issues with cookies in development.
Hack to get around same-origin cookie issue on development
Fix vagrant-specific chown so Travis will work too
debugging? we don't need no stinking debugging!
Merge pull request #594 from freedomofpress/better-config

Better config