[Task] Create local user-level configuration system

Description

As a user I would like to be able to configure certain settings of the app, such as light/dark theme preferences and preferences on whether they want to be warned about running MCP servers before quitting the app.

Having this settings file would also enable users to synchronize or back up their settings using tools specifically designed for that (such as chezmoi)

Acceptance Criteria

• Instead of using the local storage API, a real config file is used to save user preferences. Alternatively, we can use some mechanism to synchronize local storage and a config file
• The usage of this config file should be properly documented, and it should be easy for the user to figure out the location of this file
• When the user first opens the app, an empty config file should be automatically created

Priority

Low

Task Type

Feature

Additional Context

No response