docs: delete metagraph.md, migrate data model into metagraph-module.md

The historical reference doc was exactly the confusing artifact we were
cleaning up. Its unique content (the three-level type system overview
and ASCII diagram) now lives in metagraph-module.md as an introductory
section. Everything else was redundant:

- Schema types → metagraph-module.md (Module entries)
- SchemaBuilder → metagraph-module.md (SchemaBuilder Equivalence section)
- Usage patterns → metagraph-module.md + encrypted-data.md (Module examples)
- Composite identity / attributes storage → sqlite-host.md (table definitions)
- Versioning → schema-evolution.md (thorough treatment)
- Ecosystem context → overview.md (Ecosystem Integration section)

All cross-references updated: AGENTS.md, sqlite-host.md, schema-evolution.md.

docs/architecture/sqlite-host.md

@@ -136,7 +136,7 @@ node type is a valid endpoint — matching the behavior of `undefined` in the
 listed node types. There is no "no types allowed" state; if edge types need to
 be disabled, use a status or soft-delete pattern on the edge type definition.
 The repository layer must enforce this convention consistently. See
-[metagraph.md](./metagraph.md) for the schema-layer definition.
+[metagraph-module.md](./metagraph-module.md) for edge endpoint semantics.
 
 ### `graphs`