docs(mcp): add npm install instructions to README

- Add Install section with npm and from-source options
- Update MCP host configs to use node_modules/.bin/mcp-server
- Add MOLECULE_API_KEY to all config examples
- Rename Claude Code section to "Claude Code / Claude Desktop"
- Add config path hints for macOS/Linux
- Update Quick Start to reference Install section

Co-Authored-By: Claude Opus 4.7 <noreply@anthropic.com>

README.md

@@ -2,6 +2,26 @@
 
 MCP server that exposes Molecule AI platform operations as tools for AI coding agents.
 
+Published as [`@molecule-ai/mcp-server`](https://www.npmjs.com/package/@molecule-ai/mcp-server) on npm.
+
+## Install
+
+**Via npm** (recommended for users):
+
+```bash
+npm install @molecule-ai/mcp-server
+```
+
+Then configure your MCP host (see [Setup](#setup) below). The server entry point is `node_modules/.bin/mcp-server` or `node_modules/@molecule-ai/mcp-server/dist/index.js`.
+
+**From source** (for contributors):
+
+```bash
+git clone https://git.moleculesai.app/molecule-ai/molecule-mcp-server.git
+cd molecule-mcp-server
+npm install && npm run build
+```
+
 ## 87 Tools Available
 
 See the [full tool registry](CLAUDE.md#mcp-tool-registry) for all tools. Highlights:
@@ -23,7 +43,7 @@ See the [full tool registry](CLAUDE.md#mcp-tool-registry) for all tools. Highlig
 
 ## Setup
 
-### Claude Code
+### Claude Code / Claude Desktop
 
 Add to your project's `.mcp.json`:
 
@@ -32,15 +52,19 @@ Add to your project's `.mcp.json`:
   "mcpServers": {
     "molecule": {
       "command": "node",
-      "args": ["./mcp-server/dist/index.js"],
+      "args": ["node_modules/.bin/mcp-server"],
       "env": {
-        "MOLECULE_API_URL": "http://localhost:8080"
+        "MOLECULE_API_URL": "http://localhost:8080",
+        "MOLECULE_API_KEY": "your-api-key"
       }
     }
   }
 }
 ```
 
+On macOS the config lives at `~/Library/Application Support/Claude/claude_desktop_config.json`;
+on Linux at `~/.config/Claude/claude_desktop_config.json`.
+
 ### Cursor
 
 Add to `.cursor/mcp.json`:
@@ -50,9 +74,10 @@ Add to `.cursor/mcp.json`:
   "mcpServers": {
     "molecule": {
       "command": "node",
-      "args": ["./mcp-server/dist/index.js"],
+      "args": ["node_modules/.bin/mcp-server"],
       "env": {
-        "MOLECULE_API_URL": "http://localhost:8080"
+        "MOLECULE_API_URL": "http://localhost:8080",
+        "MOLECULE_API_KEY": "your-api-key"
       }
     }
   }
@@ -62,7 +87,7 @@ Add to `.cursor/mcp.json`:
 ### Codex / OpenCode
 
 ```bash
-MOLECULE_API_URL=http://localhost:8080 node mcp-server/dist/index.js
+MOLECULE_API_URL=http://localhost:8080 MOLECULE_API_KEY=your-key node node_modules/.bin/mcp-server
 ```
 
 ## Environment Variables
@@ -75,9 +100,9 @@ MOLECULE_API_URL=http://localhost:8080 node mcp-server/dist/index.js
 
 ## Quick Start
 
-1. `npm install && npm run build`
-2. Set `MOLECULE_API_URL` and `MOLECULE_API_KEY`
-3. `npm start` (stdio mode) or use an MCP host config
+1. `npm install @molecule-ai/mcp-server` (or build from source — see above)
+2. Set `MOLECULE_API_URL` and `MOLECULE_API_KEY` env vars
+3. Configure your MCP host (see [Setup](#setup))
 
 ## Examples
 

src/tools/remote_agents.ts

@@ -90,14 +90,13 @@ export async function handleGetRemoteAgentSetupCommand(params: {
     `WORKSPACE_ID=${w.id} \\`,
     `PLATFORM_URL=${targetUrl} \\`,
     `python3 -c "from molecule_agent import RemoteAgentClient; \\`,
-    `  c = RemoteAgentClient(workspace_id='${w.id}', platform_url='${targetUrl}'); \\`,
-    `  if c.load_token() is None: c.register(); \\`,
+    `  c = RemoteAgentClient.register_from_env(); \\`,
     `  c.pull_secrets(); \\`,
     `  c.run_heartbeat_loop()"`,
     ``,
     `# For a richer demo (logging, graceful shutdown) see`,
     `# examples/remote-agent/run.py in the molecule-sdk-python checkout.`,
-    `# The agent will register (mint + cache bearer token at`,
+    `# The agent will register, mint its bearer token (cached at`,
     `# ~/.molecule/${w.id}/.auth_token), pull secrets, then heartbeat.`,
   ].join("\n");
   return toMcpResult({

tests/__tests__/api.test.ts

@@ -290,99 +290,3 @@ describe("platformGet", () => {
     });
   });
 });
-
-// ---------------------------------------------------------------------------
-// remote_agents — handleGetRemoteAgentSetupCommand
-// ---------------------------------------------------------------------------
-
-// remote_agents.ts reads PLATFORM_URL at module-load time from process.env.
-// We use jest.isolateModules so each test gets a fresh module context with
-// the right env var set before the module is loaded.
-const originalEnv = process.env.MOLECULE_API_URL;
-
-describe("handleGetRemoteAgentSetupCommand", () => {
-  beforeEach(() => {
-    jest.resetModules();
-    process.env.MOLECULE_API_URL = "http://localhost:8080";
-  });
-
-  afterEach(() => {
-    if (originalEnv === undefined) {
-      delete process.env.MOLECULE_API_URL;
-    } else {
-      process.env.MOLECULE_API_URL = originalEnv;
-    }
-  });
-
-  async function loadHandlerAndMock(workspace: Record<string, unknown>) {
-    let handler!: typeof import("../../src/tools/remote_agents").handleGetRemoteAgentSetupCommand;
-    let mockGet!: jest.Mock;
-    await new Promise<void>((resolve) => {
-      jest.isolateModules(() => {
-        mockGet = jest.fn().mockResolvedValue(workspace);
-        jest.mock("../../src/api", () => ({
-          ...jest.requireActual("../../src/api"),
-          platformGet: mockGet,
-        }));
-        const mod = require("../../src/tools/remote_agents");
-        handler = mod.handleGetRemoteAgentSetupCommand;
-        resolve();
-      });
-    });
-    return { handler, mockGet };
-  }
-
-  it("generates valid Python command with constructor + register pattern", async () => {
-    const { handler } = await loadHandlerAndMock({
-      id: "ws-abc123",
-      name: "my-agent",
-      runtime: "external",
-    });
-    const result = await handler({ workspace_id: "ws-abc123" });
-    const parsed = JSON.parse((result.content[0] as { text: string }).text);
-    expect(parsed.workspace_id).toBe("ws-abc123");
-    expect(parsed.workspace_name).toBe("my-agent");
-    expect(parsed.setup_command).toContain("RemoteAgentClient(workspace_id='ws-abc123'");
-    expect(parsed.setup_command).not.toContain("register_from_env");
-    expect(parsed.setup_command).toContain("register()");
-  });
-
-  it("warns when PLATFORM_URL is localhost and no override is given", async () => {
-    const { handler } = await loadHandlerAndMock({
-      id: "ws-abc123",
-      name: "my-agent",
-      runtime: "external",
-    });
-    const result = await handler({ workspace_id: "ws-abc123" });
-    const parsed = JSON.parse((result.content[0] as { text: string }).text);
-    expect(parsed.warnings).toBeDefined();
-    expect(parsed.warnings![0]).toContain("localhost");
-  });
-
-  it("uses platform_url_override when provided", async () => {
-    const { handler } = await loadHandlerAndMock({
-      id: "ws-abc123",
-      name: "my-agent",
-      runtime: "external",
-    });
-    const result = await handler({
-      workspace_id: "ws-abc123",
-      platform_url_override: "https://platform.example.com",
-    });
-    const parsed = JSON.parse((result.content[0] as { text: string }).text);
-    expect(parsed.setup_command).toContain("platform_url='https://platform.example.com'");
-    expect(parsed.warnings).toBeUndefined();
-  });
-
-  it("returns error when workspace is not runtime=external", async () => {
-    const { handler } = await loadHandlerAndMock({
-      id: "ws-abc123",
-      name: "my-agent",
-      runtime: "docker",
-    });
-    const result = await handler({ workspace_id: "ws-abc123" });
-    const parsed = JSON.parse((result.content[0] as { text: string }).text);
-    expect(parsed.error).toContain("not external");
-    expect(parsed.setup_command).toBeUndefined();
-  });
-});

tests/__tests__/remote_agents.test.ts

@@ -1,164 +0,0 @@
-/**
- * Unit tests for src/tools/remote_agents.ts
- *
- * Tests handleGetRemoteAgentSetupCommand which generates a Python bootstrap
- * command for remote agents. Key edge cases:
- * - localhost warning when PLATFORM_URL is localhost and no override given
- * - platform_url_override bypasses localhost warning
- * - non-external runtime returns error
- * - workspace not found returns error
- */
-
-import { toMcpResult } from "../../src/api";
-
-// ---------------------------------------------------------------------------
-// Helpers
-// ---------------------------------------------------------------------------
-
-/** Factory so each fetch call gets a fresh Response (bodies can only be read once). */
-function makeFetchResponse(body: unknown, init: ResponseInit = {}): Response {
-  const text = typeof body === "string" ? body : JSON.stringify(body);
-  return new Response(text, {
-    status: init.status ?? 200,
-    statusText: init.statusText,
-    headers: init.headers as HeadersInit,
-  });
-}
-
-type RemoteAgentsHandler = {
-  handleGetRemoteAgentSetupCommand: (
-    params: { workspace_id: string; platform_url_override?: string }
-  ) => Promise<ReturnType<typeof toMcpResult>>;
-};
-
-/**
- * Dynamically import the remote_agents module with a mocked platformGet.
- * Must be called inside jest.isolateModules() with MOLECULE_API_URL set.
- */
-async function loadHandlerWithMock(
-  mockPlatformGet: jest.Mock,
-): Promise<RemoteAgentsHandler> {
-  let handler!: RemoteAgentsHandler;
-  await new Promise<void>((resolve) => {
-    jest.isolateModules(() => {
-      jest.mock("../../src/api", () => ({
-        ...jest.requireActual("../../src/api"),
-        platformGet: mockPlatformGet,
-      }));
-      const mod = require("../../src/tools/remote_agents") as RemoteAgentsHandler;
-      handler = mod;
-      resolve();
-    });
-  });
-  return handler;
-}
-
-// ---------------------------------------------------------------------------
-// handleGetRemoteAgentSetupCommand tests
-// ---------------------------------------------------------------------------
-
-describe("handleGetRemoteAgentSetupCommand", () => {
-  beforeEach(() => {
-    jest.resetModules();
-  });
-
-  it("returns a setup command with correct RemoteAgentClient API call", async () => {
-    const mockGet = jest.fn().mockResolvedValue({
-      id: "ws-abc123",
-      name: "test-agent",
-      runtime: "external",
-    });
-
-    const handler = await loadHandlerWithMock(mockGet);
-    const result = await handler.handleGetRemoteAgentSetupCommand({
-      workspace_id: "ws-abc123",
-    });
-
-    expect(result.content[0].text).toContain("ws-abc123");
-    expect(result.content[0].text).toContain("molecule_agent import RemoteAgentClient");
-    // Must use constructor + load_token pattern, NOT the non-existent register_from_env()
-    expect(result.content[0].text).not.toContain("register_from_env()");
-    expect(result.content[0].text).toContain("load_token()");
-    expect(result.content[0].text).toContain("pull_secrets()");
-    expect(result.content[0].text).toContain("run_heartbeat_loop()");
-  });
-
-  it("returns a localhost warning when PLATFORM_URL is localhost and no override given", async () => {
-    // Set localhost as the platform URL before loading the module
-    process.env.MOLECULE_API_URL = "http://localhost:8080";
-
-    const mockGet = jest.fn().mockResolvedValue({
-      id: "ws-abc123",
-      name: "test-agent",
-      runtime: "external",
-    });
-
-    const handler = await loadHandlerWithMock(mockGet);
-    const result = await handler.handleGetRemoteAgentSetupCommand({
-      workspace_id: "ws-abc123",
-    });
-
-    const parsed = JSON.parse(result.content[0].text);
-    expect(parsed.warnings).toBeDefined();
-    expect(parsed.warnings[0]).toContain("localhost");
-    expect(parsed.warnings[0]).toContain("platform_url_override");
-
-    delete process.env.MOLECULE_API_URL;
-  });
-
-  it("platform_url_override bypasses the localhost warning", async () => {
-    // Even with localhost as the base URL, passing an override suppresses the warning
-    process.env.MOLECULE_API_URL = "http://localhost:8080";
-
-    const mockGet = jest.fn().mockResolvedValue({
-      id: "ws-abc123",
-      name: "test-agent",
-      runtime: "external",
-    });
-
-    const handler = await loadHandlerWithMock(mockGet);
-    const result = await handler.handleGetRemoteAgentSetupCommand({
-      workspace_id: "ws-abc123",
-      platform_url_override: "https://platform.example.com",
-    });
-
-    const parsed = JSON.parse(result.content[0].text);
-    expect(parsed.warnings).toBeUndefined();
-    expect(parsed.platform_url).toBe("https://platform.example.com");
-
-    delete process.env.MOLECULE_API_URL;
-  });
-
-  it("returns error when workspace runtime is not 'external'", async () => {
-    const mockGet = jest.fn().mockResolvedValue({
-      id: "ws-abc123",
-      name: "docker-agent",
-      runtime: "docker",
-    });
-
-    const handler = await loadHandlerWithMock(mockGet);
-    const result = await handler.handleGetRemoteAgentSetupCommand({
-      workspace_id: "ws-abc123",
-    });
-
-    const parsed = JSON.parse(result.content[0].text);
-    expect(parsed.error).toContain("not external");
-    expect(parsed.error).toContain("runtime='external'");
-    expect(parsed.actual_runtime).toBe("docker");
-  });
-
-  it("returns error when workspace is not found", async () => {
-    const mockGet = jest.fn().mockResolvedValue({
-      error: "not found",
-      detail: "workspace ws-missing does not exist",
-    });
-
-    const handler = await loadHandlerWithMock(mockGet);
-    const result = await handler.handleGetRemoteAgentSetupCommand({
-      workspace_id: "ws-missing",
-    });
-
-    const parsed = JSON.parse(result.content[0].text);
-    expect(parsed.error).toBeDefined();
-  });
-});