The hierarchical system I've developed organizes knowledge in nested MECE categories (Mutually Exclusive, Collectively Exhaustive). Rather than paralleling code exactly, it creates a conceptual tree that represents the mental model behind the system.

For example, in an e-commerce API: - Level 1: Core domains (Products, Orders, Users) - Level 2: Sub-domains (Product variants, Order fulfillment, User authentication) - Level 3: Implementation details (Variant pricing logic, Fulfillment status transitions)

I'm currently using plain Markdown with a specific folder structure, making it friendly to version control and AI tools. The key innovation is the organization pattern rather than the tooling - ensuring each concept belongs in exactly one place (mutually exclusive) while collectively covering all needed context (collectively exhaustive).

I should note that this is a work in progress - I've documented the vision and principles, but the implementation is still evolving. The early results are promising though: AI assistants navigating this conceptual tree find the context needed for specific coding tasks more effectively, significantly improving the quality of generated code.