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/protocol/src/thread-index.ts

@@ -50,7 +50,7 @@ export function markThreadSuspended(
   };
 }
 
-/** Serialize for threads.yaml — compact string when not suspended. */
+/** Serialize for variable store — compact string when not suspended. */
 export function serializeThreadIndexEntry(
   entry: ThreadIndexEntry,
 ): string | Record<string, string> {

packages/protocol/src/types.ts

@@ -113,7 +113,7 @@ export type StepOutput = {
   background: boolean | null;
 };
 
-/** Active thread entry in ~/.uwf/threads.yaml */
+/** Active thread entry in @uwf/thread/* variable store */
 export type ThreadIndexEntry = {
   head: CasRef;
   suspendedRole: string | null;
@@ -210,5 +210,5 @@ export type WorkflowConfig = {
   modelOverrides: Record<Scenario, ModelAlias> | null;
 };
 
-/** ~/.uwf/threads.yaml */
+/** @uwf/thread/* variable store index */
 export type ThreadsIndex = Record<ThreadId, ThreadIndexEntry>;