fix(docs): remove non-existent HTTP/SSE transport and MCP_SERVER_PORT

MCP server source confirms:
- Only StdioServerTransport exists (no HTTP/SSE server)
- No MCP_SERVER_PORT env var
- apiCall() sends no Authorization header

Removed the entire "Transport modes" section (non-existent HTTP/SSE
endpoint), MCP_SERVER_PORT row from env table and troubleshooting, and
MOLECULE_API_KEY from config examples (auth is planned, not wired yet).
Replaced with accurate "Transport" section documenting stdio-only mode.

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

content/docs/mcp-server.mdx

@@ -25,8 +25,7 @@ npx @molecule-ai/mcp-server@1.0.0
       "command": "npx",
       "args": ["@molecule-ai/mcp-server@1.0.0"],
       "env": {
-        "MOLECULE_URL": "http://localhost:8080",
-        "MOLECULE_API_KEY": "your-bearer-token"
+        "MOLECULE_URL": "http://localhost:8080"
       }
     }
   }
@@ -37,13 +36,14 @@ npx @molecule-ai/mcp-server@1.0.0
   **Pin the package version.** The examples above use `@1.0.0` — always specify an exact version and omit the `-y` flag. An unpinned `npx -y @molecule-ai/mcp-server` (no version) silently installs whatever npm serves on the next restart; if the package is ever compromised, it runs with your full MCP client permissions. Check [npm](https://www.npmjs.com/package/@molecule-ai/mcp-server) for the latest stable release before upgrading.
 </Callout>
 
-For SaaS deployments, set `MOLECULE_URL` to your tenant URL and add your API key:
+For SaaS deployments, set `MOLECULE_URL` to your tenant URL:
 
 ```json
-"MOLECULE_URL": "https://your-org.moleculesai.app",
-"MOLECULE_API_KEY": "your-bearer-token"
+"MOLECULE_URL": "https://your-org.moleculesai.app"
 ```
 
+Auth via `MOLECULE_API_KEY` is planned for a future release.
+
 ### Verify
 
 Once configured, your MCP client should show 87 Molecule AI tools. Test with:
@@ -154,34 +154,11 @@ The MCP server exposes tools across these categories:
 | Variable | Default | Description |
 |---|---|---|
 | `MOLECULE_URL` | `http://localhost:8080` | Platform API URL |
-| `MOLECULE_API_KEY` | — | Bearer token for platform authentication |
-| `MCP_SERVER_PORT` | `3000` | TCP port for HTTP/SSE transport |
+| `MOLECULE_API_KEY` | — | Bearer token for platform authentication (planned) |
 
-## Transport modes
+## Transport
 
-The MCP server supports two transport modes:
-
-### stdio (default, for local AI clients)
-
-Claude Code, Cursor, and similar local AI clients use stdio transport. The client spawns the MCP server as a child process and communicates via JSON-RPC over stdin/stdout. Configure in your AI client's `mcp.json` as shown in Quick start above.
-
-### HTTP/SSE (for remote agents and headless clients)
-
-For agents running on remote servers or in environments where stdio is not available, the MCP server exposes an HTTP endpoint with Server-Sent Events (SSE) for streaming responses. The agent card and tool responses are available at:
-
-```
-http://localhost:3000/agent/card   # MCP server info + tool manifest
-http://localhost:3000/             # SSE stream for responses
-```
-
-Start the server in HTTP/SSE mode:
-
-```bash
-MCP_SERVER_PORT=3000 npm start
-# Server starts on http://localhost:3000
-```
-
-Configure your MCP client to connect over HTTP. The server emits `data: null` heartbeats every 30 seconds on idle connections to keep proxies and load balancers from closing the SSE stream.
+The MCP server uses **stdio transport** — the client (Claude Code, Cursor, etc.) spawns the server as a child process and communicates via JSON-RPC over stdin/stdout. Configure in your AI client's `mcp.json` as shown in Quick start above.
 
 ## Troubleshooting
 
@@ -189,5 +166,4 @@ Configure your MCP client to connect over HTTP. The server emits `data: null` he
 |---|---|
 | Connection refused | Check `MOLECULE_URL` points to running platform |
 | 401 Unauthorized | Token expired or revoked — create a new one |
-| Port already in use | Set `MCP_SERVER_PORT` to an available port if 3000 is taken |
 | Tools not showing | Run `npx @molecule-ai/mcp-server@1.0.0` standalone to check errors |