refactor(coding-agent/core): simplified Python gateway coordination by removing reference counting

- Simplified Python gateway coordination by removing reference counting and idle timeout functionality.
- Updated Python kernel initialization to support environment variable setup and working directory configuration.
- Modified interactive status display to show Python and venv paths instead of client counts.
- Updated system prompt to clarify CHECKPOINT step 0 timing after user request completion.

packages/coding-agent/test/tools/python.test.ts

@@ -57,7 +57,7 @@ describe("python tool schema", () => {
 
 		expect(schema.type).toBe("object");
 		expect(schema.properties.cells.type).toBe("array");
-		expect(schema.properties.timeout_ms.type).toBe("number");
+		expect(schema.properties.timeout.type).toBe("number");
 		expect(schema.properties.cwd.type).toBe("string");
 		expect(schema.properties.reset.type).toBe("boolean");
 		expect(schema.required).toEqual(["cells"]);