docs: update stale comments and prompts referencing old storage formats

- architecture-reference.ts: threads.yaml/history.jsonl/registry.yaml → variable store, storage layout updated (~/.ocas/ + ~/.uwf/)
- protocol types.ts: JSDoc comments updated
- thread-index.ts: serialization comment updated
- util-agent context.ts: buildContext JSDoc updated

Only migration code in store.ts retains old file references (needed to read legacy files).

packages/util-agent/src/context.ts

@@ -150,7 +150,7 @@ async function loadWorkflow(store: Store, schemas: AgentStore["schemas"], workfl
 }
 
 /**
- * Build agent execution context from thread head in threads.yaml.
+ * Build agent execution context from thread head in the variable store.
  * Walks the CAS chain from head to StartNode and expands step outputs.
  */
 export async function buildContext(