Storage ports: ChatStore/GraphStore/JobStore + adapters + core inversion (stage 3)

Per-entity semantic ports (src/core/ports.ts), one adapter family
(src/store/*, fs JSON/JSONL), exactly one composition point
(src/server/stores.ts). Dependency direction is now machine-checked:
adapters implement core interfaces; core never imports an adapter.

The inversion:
- core/graph.ts (emitChat/getGraph/graphSnapshot/foldStaleChats) is now
  pure — it takes the storage ports as explicit parameters (GraphDeps).
  No store imports; newGraphNodeId is local; node id format unchanged.
- core/graph-context.ts buildGraphContext() no longer defaults to the
  live ledgers: the chat-handler hands in getGraph(graphStore) per turn.
- store adapters export exactly one object each implementing their port
  (chatStore/graphStore/jobStore); bodies otherwise verbatim.
  NodeMapping + SessionCheckpoint moved store/graph -> core/contracts
  (they ARE contract shapes); CreateJobInit/JobPatch live in ports.
- titleFromPrompt moved store/chats -> core/contracts (pure helper,
  planNodeStatus precedent). Store modules now contain persistence only.
- server/stores.ts is the composition root; server/{chats,graph,jobs}.ts
  and chat-handler wire from it; agent (plan tools, sub-agent runner)
  call the port objects. The shell surface (@/src/server exports) is
  unchanged.

Lint law extended: the whole of src/core is now a purity zone (was a
file glob with a graph/graph-context exemption). Verified it fires on
core->store imports; tsc clean, 190/190 tests, eslint clean, prod build
clean (prerender 6/6). Tests pass deps explicitly — graph.test uses the
same fs-adapter pair stores.ts wires in production; graph-context.test
keeps its in-memory ledgers as a GraphStore implementation.

src/server/chat-handler.ts

@@ -2,9 +2,9 @@ import { createAgentUIStreamResponse, type UIMessage } from "ai";
 import { createTeacherAgent, type TeacherAgent } from "../agent/teacher-agent.ts";
 import { createTeacherTools } from "../agent/tools.ts";
 import { spawnPendingJobs } from "../agent/subagents/runner.ts";
-import { emitChat } from "../core/graph.ts";
+import { emitChat, getGraph } from "../core/graph.ts";
 import { buildGraphContext } from "../core/graph-context.ts";
-import { getChat, saveMessages } from "../store/chats.ts";
+import { stores } from "./stores.ts";
 
 /**
  * One chat turn: run the teacher agent over the client's message list and
@@ -23,7 +23,7 @@ export async function handleChatRequest(req: Request, agent?: TeacherAgent): Pro
 		return Response.json({ error: "Invalid JSON body" }, { status: 400 });
 	}
 	const chatId = typeof body.chatId === "string" ? body.chatId : "";
-	if (!chatId || !getChat(chatId)) {
+	if (!chatId || !stores.chatStore.getChat(chatId)) {
 		return Response.json({ error: "Unknown chat" }, { status: 404 });
 	}
 	if (!Array.isArray(body.messages)) {
@@ -37,7 +37,7 @@ export async function handleChatRequest(req: Request, agent?: TeacherAgent): Pro
 	// take the lesson down: the block is context, not a dependency.
 	let graphContext: string | null = null;
 	try {
-		graphContext = buildGraphContext();
+		graphContext = buildGraphContext(getGraph(stores.graphStore));
 	} catch (err) {
 		console.error(`[chat ${chatId}] graph context build failed:`, err);
 	}
@@ -49,7 +49,7 @@ export async function handleChatRequest(req: Request, agent?: TeacherAgent): Pro
 			// Persist even when aborted: the partial transcript (including any
 			// pending question part) is what makes resume work.
 			try {
-				saveMessages(chatId, messages as UIMessage[]);
+				stores.chatStore.saveMessages(chatId, messages as UIMessage[]);
 			} catch (err) {
 				console.error(`[chat ${chatId}] persist failed:`, err, { isAborted });
 			}
@@ -67,7 +67,7 @@ export async function handleChatRequest(req: Request, agent?: TeacherAgent): Pro
 			// Skipped under tests: scripted chats are fixtures, not knowledge.
 			if (process.env.NODE_ENV !== "test") {
 				try {
-					emitChat(chatId);
+					emitChat(chatId, stores);
 				} catch (err) {
 					console.error(`[chat ${chatId}] graph emission failed:`, err);
 				}

src/server/chats.ts

@@ -1,9 +1,11 @@
-import { createChat, getChat, listChats, titleFromPrompt } from "../store/chats.ts";
+import { stores } from "./stores.ts";
+import { titleFromPrompt } from "../core/contracts.ts";
 
 /**
  * Server-side chat entries for the transport layer (app/api/chats*,
- * app/chat/[id]). Today these delegate straight to the fs store; the
+ * app/chat/[id]). Today these delegate straight to the ChatStore port; the
  * services stage carves the real orchestration behind this same surface.
  */
 
-export { createChat, getChat, listChats, titleFromPrompt };
+export const { createChat, getChat, listChats } = stores.chatStore;
+export { titleFromPrompt };

src/server/graph.ts

@@ -1,5 +1,6 @@
 import type { GraphSnapshot } from "../core/contracts.ts";
 import { foldStaleChats, graphSnapshot } from "../core/graph.ts";
+import { stores } from "./stores.ts";
 
 /**
  * Server-side graph entry for the home view (GET /api/graph): fold any chat
@@ -9,6 +10,6 @@ import { foldStaleChats, graphSnapshot } from "../core/graph.ts";
  * same read surface.
  */
 export function graphView(): GraphSnapshot {
-	foldStaleChats();
-	return graphSnapshot();
+	foldStaleChats(stores);
+	return graphSnapshot(stores);
 }

src/server/index.ts

@@ -8,3 +8,4 @@ export * from "./chat-handler.ts";
 export * from "./chats.ts";
 export * from "./graph.ts";
 export * from "./jobs.ts";
+export * from "./stores.ts";

src/server/jobs.ts

@@ -1,4 +1,4 @@
-import { listJobs } from "../store/jobs.ts";
+import { stores } from "./stores.ts";
 
 /**
  * Server-side job-status entry (GET /api/jobs?chatId=…, contracts.ts
@@ -7,4 +7,4 @@ import { listJobs } from "../store/jobs.ts";
  * re-syncs the chat when the job flips to done/error.
  */
 
-export { listJobs };
+export const { listJobs } = stores.jobStore;

src/server/stores.ts

@@ -0,0 +1,19 @@
+/**
+ * THE COMPOSITION ROOT for storage — the single place concrete store
+ * adapters are wired. Everything else (core, services, agents) codes against
+ * the port types in core/ports.ts and receives instances through this
+ * module. Swapping the fs adapter for SQLite later changes exactly this
+ * file (and the adapter implementations in src/store/).
+ */
+
+import { chatStore } from "../store/chats.ts";
+import { graphStore } from "../store/graph.ts";
+import { jobStore } from "../store/jobs.ts";
+/** The wired adapters. Satisfies core/graph.ts's GraphDeps structurally. */
+export const stores = {
+	chatStore,
+	graphStore,
+	jobStore,
+};
+
+export type Stores = typeof stores;