Beginner Issue: Refresh the README data-storage/schema documentation to match the current SQLite + YAML design

[ambicuity]

Type

Documentation

Area

Documentation

Difficulty

Beginner

Maintainer Guidance Needed

Medium

Problem

The README schema diagram is stale relative to the current implementation. It still implies structures like a collections table and outdated document fields, while the real system stores collection config in YAML and uses separate content, documents, content_vectors, and llm_cache tables with different column names.

Why It Matters

Architecture docs should help contributors orient themselves. A stale schema sends people to the wrong mental model before they ever open engine/repository.ts.

Scope

Update the README data-storage section and schema diagram so it accurately reflects the current storage model, including the role of YAML config versus SQLite tables.

Acceptance Criteria

• The README schema description matches the current tables created in engine/repository.ts.
• The docs no longer imply that collection config lives in SQLite.
• The data-storage section mentions the YAML catalog as part of the system design.

Relevant Files

• README.md
• engine/repository.ts
• engine/catalogs.ts

Testing

• Cross-check the updated README against the schema creation code in engine/repository.ts.
• Run npm run build.

Non-goals

• Redesigning the database schema
• Adding new migration docs
• Writing a full low-level schema reference for every table and index

Difficulty Rationale

This is documentation work, but it requires enough repo familiarity to reconcile docs with the live schema and config model.

Checklist

• I searched open and recently closed issues before drafting this task.
• The issue is scoped to one focused PR.
• The likely files and verification steps are listed.