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/agent-runtime/workspace-runtime.md

@@ -42,7 +42,7 @@ Common runtime environment variables:
 ```bash
 WORKSPACE_ID=ws-123
 WORKSPACE_CONFIG_PATH=/configs
-PLATFORM_URL=http://host.docker.internal:8080
+PLATFORM_URL=http://platform:8080
 PARENT_ID=
 AWARENESS_URL=http://awareness:37800
 AWARENESS_NAMESPACE=workspace:ws-123

content/docs/architecture/molecule-technical-doc.md

@@ -929,7 +929,7 @@ Postgres + Redis + Langfuse only (for local development without containerized wo
 |----------|---------|---------|
 | `WORKSPACE_ID` | `workspace-default` | Unique workspace identifier |
 | `WORKSPACE_CONFIG_PATH` | `/configs` | Config directory mount |
-| `PLATFORM_URL` | `http://host.docker.internal:8080` | Platform connection |
+| `PLATFORM_URL` | `http://platform:8080` | Platform connection |
 | `PARENT_ID` | Empty | Parent workspace ID (set if nested) |
 | `AWARENESS_URL` | Optional | Awareness service |
 | `AWARENESS_NAMESPACE` | Optional | Scoped namespace for awareness memory |

content/docs/development/local-development.md

@@ -66,7 +66,7 @@ WORKSPACE_ID=           # assigned by platform on provision
 WORKSPACE_CONFIG_PATH=  # path to config folder inside container
 MODEL_PROVIDER=         # e.g. anthropic:claude-sonnet-4-6
 TIER=                   # 1, 2, 3, or 4
-PLATFORM_URL=           # http://host.docker.internal:8080 (in Docker) or http://localhost:8080 (on host)
+PLATFORM_URL=           # http://platform:8080
 PARENT_ID=              # set by platform during team expansion (empty for top-level)
 ANTHROPIC_API_KEY=      # or OPENAI_API_KEY, etc.
 LANGFUSE_HOST=          # http://langfuse-web:3000 (internal container port; host-mapped to :3001)

content/docs/mcp-server.mdx

@@ -42,6 +42,8 @@ For SaaS deployments, set `MOLECULE_URL` to your tenant URL:
 "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:
@@ -152,6 +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 (planned) |
+
+## Transport
+
+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