Upgradable default config values/profiles

Currently, profiles and many of our default config values are written to the config. Unfortunately, this makes it hard for us to _change_ them for existing users, even when the user hasn't explicitly chosen to override something.

Proposal:

1. Mostly empty on-disk config by default.
2. Add a "profiles" section to the config that lists all the profiles that should be applied and in what order.
3. Add "DefaultX: bool"/"CustomX: value" options where applicable (e.g., bootstrappers), to allow users to extend defaults.

At runtime, we'd:

1. Read the config.
2. Apply the defaults to the in-memory config.
3. Apply the profiles to the in-memory config.

When updating the config, we'd:

1. Re-read the on-disk config.
2. Apply the update to the on-disk config without persisting the in-memory config (unless necessary?).