diff --git a/.vscode/launch.json b/.vscode/launch.json
index 5a5e281..9052474 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -2,11 +2,10 @@
   "version": "0.2.0",
   "configurations": [
     {
-      "name": "Debug: Agent",
+      "name": "Debug: MCP Server",
       "type": "bun",
       "request": "launch",
-      "program": "${workspaceFolder}/agent.ts",
-      "args": ["How does array DefineOwnProperty work?"],
+      "program": "${workspaceFolder}/src/mcp-server.ts",
       "cwd": "${workspaceFolder}",
       "stopOnEntry": false,
       "watchMode": false
@@ -15,17 +14,7 @@
       "name": "Debug: Ingest",
       "type": "bun",
       "request": "launch",
-      "program": "${workspaceFolder}/setup/ingest.ts",
-      "cwd": "${workspaceFolder}",
-      "stopOnEntry": false,
-      "watchMode": false
-    },
-    {
-      "name": "Debug: Test Spec Retriever",
-      "type": "bun",
-      "request": "launch",
-      "program": "${workspaceFolder}/test/manual/test-spec-retriever.ts",
-      "args": ["array.[[DefineOwnProperty]]"],
+      "program": "${workspaceFolder}/src/setup/ingest.ts",
       "cwd": "${workspaceFolder}",
       "stopOnEntry": false,
       "watchMode": false
@@ -34,7 +23,7 @@
       "name": "Debug: Build Graph",
       "type": "bun",
       "request": "launch",
-      "program": "${workspaceFolder}/setup/buildGraph.ts",
+      "program": "${workspaceFolder}/src/setup/buildGraph.ts",
       "cwd": "${workspaceFolder}",
       "stopOnEntry": false,
       "watchMode": false
diff --git a/src/agent.ts b/src/agent.ts
deleted file mode 100644
index c26451e..0000000
--- a/src/agent.ts
+++ /dev/null
@@ -1,119 +0,0 @@
-import fs from "node:fs";
-import * as lancedbSdk from "@lancedb/lancedb";
-import { LanceDB } from "@langchain/community/vectorstores/lancedb";
-import { ChatPromptTemplate } from "@langchain/core/prompts";
-import { OllamaEmbeddings } from "@langchain/ollama";
-import { ChatOpenAI } from "@langchain/openai";
-import Graph from "graphology";
-import { AgentExecutor, createReactAgent } from "langchain/agents";
-import {
-  createEvaluateInEngine262Tool,
-  createGetSectionContentTool,
-  createGraphExplorerTool,
-  createSearchSpecSectionsTool,
-} from "./agent-tools/index.js";
-import {
-  CONFIG_FILE,
-  EMBEDDING_MODEL,
-  GRAPH_FILE,
-  STORAGE_DIR,
-} from "./constants.js";
-
-const embeddings = new OllamaEmbeddings({
-  model: EMBEDDING_MODEL,
-});
-
-const config = JSON.parse(fs.readFileSync(CONFIG_FILE, "utf-8"));
-const apiKey = config.NVIDIA_API_KEY;
-const baseURL = config.NVIDIA_API_BASE;
-
-if (!apiKey) {
-  console.warn("Please set NVIDIA_API_KEY in config.json.");
-}
-
-const llm = new ChatOpenAI({
-  modelName: "openai/gpt-oss-120b",
-  openAIApiKey: apiKey,
-  configuration: { baseURL },
-  temperature: 0,
-});
-
-const systemPrompt = `You are an expert in the ECMAScript specification and its implementation in engine262.
-Your goal is to explain how specific parts of the language work by combining information from the provided tools.
-
-Available tools: {tool_names}
-{tools}
-
-CRITICAL INSTRUCTIONS:
-1. ALWAYS prefer using the provided tools ('ask262_search_spec_sections', 'ask262_get_section_content', 'ask262_graph_explorer', and 'ask262_evaluate_in_engine262') to answer questions.
-2. Do NOT rely on your internal knowledge of JavaScript or the ECMAScript specification.
-3. If the user asks about a function, you MUST first use 'ask262_search_spec_sections' to find the associated specification section.
-4. You MUST then use 'ask262_get_section_content' to read the actual text of that specification section before answering.
-5. When the user provides JavaScript code or asks about runtime behavior, use 'ask262_evaluate_in_engine262' to execute the code and see which spec sections are hit during execution.
-6. Base your explanations ONLY on the information retrieved from the tools.
-7. If the tools do not provide enough information, state that clearly rather than guessing from your internal knowledge.
-
-{agent_scratchpad}`;
-
-const prompt = ChatPromptTemplate.fromMessages([
-  ["system", systemPrompt],
-  ["human", "{input}"],
-]);
-
-async function main() {
-  console.log("Loading indices and graph...");
-
-  const db = await lancedbSdk.connect(STORAGE_DIR);
-  const table = await db.openTable("spec_vectors");
-  const vectorStore = new LanceDB(embeddings, { table });
-
-  const graphData = JSON.parse(fs.readFileSync(GRAPH_FILE, "utf-8"));
-  const graph = new Graph({ multi: true });
-  graph.import(graphData);
-
-  // Create tools using factory functions
-  const searchSpecSectionsTool = createSearchSpecSectionsTool(
-    table,
-    embeddings,
-  );
-  const getSectionContentTool = createGetSectionContentTool(table);
-  const graphTool = createGraphExplorerTool(graph);
-  const evaluateTool = createEvaluateInEngine262Tool();
-
-  const agent = await createReactAgent({
-    llm,
-    tools: [
-      searchSpecSectionsTool,
-      getSectionContentTool,
-      graphTool,
-      evaluateTool,
-    ],
-    prompt,
-  });
-
-  const agentExecutor = new AgentExecutor({
-    agent,
-    tools: [
-      searchSpecSectionsTool,
-      getSectionContentTool,
-      graphTool,
-      evaluateTool,
-    ],
-  });
-
-  console.log("Agent is ready!");
-
-  const message =
-    process.argv[2] ||
-    "Which spec section does Evaluate_IfStatement implement? and what does that section say?";
-  console.log(`User: ${message}`);
-
-  const response = await agentExecutor.invoke({
-    input: message,
-  });
-
-  console.log("\n--- Agent Response ---\n");
-  console.log(response.output);
-}
-
-main().catch(console.error);