Add experimental Docker support and update configuration handling

- Introduced `DOCKER.md` with detailed setup instructions and limitations.
- Enhanced `compose.yaml` with dynamic port and environment variable support.
- Updated `agent.py` to detect Docker environments and disable GUI features.
- Modified configuration paths to support both Docker and non-Docker setups.
- Marked Docker support as experimental in the documentation.

compose.yaml

@@ -6,8 +6,10 @@ services:
       dockerfile: Dockerfile
       target: production
     ports:
-      - "9121:9121"
-      - "24282:24282"
+      - "${SERENA_PORT:-9121}:9121"  # MCP server port
+      - "${SERENA_DASHBOARD_PORT:-24282}:24282"  # Dashboard port (default 0x5EDA = 24282)
+    environment:
+      - SERENA_DOCKER=1
     command:
       - "uv run --directory . serena-mcp-server --transport sse --port 9121 --host 0.0.0.0"
 
@@ -19,7 +21,12 @@ services:
       target: development
     tty: true
     stdin_open: true
+    environment:
+      - SERENA_DOCKER=1
     volumes:
       - .:/workspaces/serena
+    ports:
+      - "${SERENA_PORT:-9121}:9121"  # MCP server port
+      - "${SERENA_DASHBOARD_PORT:-24282}:24282"  # Dashboard port
     command:
       - "uv run --directory . serena-mcp-server"