Introduce a unified configuration system

Introduce a unified configuration database, e.g. JSON-based, where configurations could be scoped using a certain prefix.

The issue proposes a unified JSON-based configuration database with prefix-based scoping, but it names no files, tests, entry points, or acceptance criteria. First map how configuration is currently handled across the assistant, then identify the relevant configuration entry points and define the required scoping behavior before implementation. Done means configurations use one consistent system and the scoping rules are covered by tests.

Written by the indexing model from the issue text.