feat(coding-agent): added multi-cell Python execution with persistent kernel

- Added multi-cell Python execution with sequential processing in persistent kernel.
- Changed Python tool API to use cells array instead of single code parameter.
- Renamed workdir parameter to cwd across Bash and Python tools for consistency.
- Fixed indentation adjustment logic for mixed indentation levels in patch tool.

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

@@ -40,7 +40,7 @@ describe("python tool execution", () => {
 		const tool = new PythonTool(createSession(tempDir.path));
 		const result = await tool.execute(
 			"call-id",
-			{ code: "print('hi')", timeoutMs: 5000, workdir: tempDir.path, reset: true },
+			{ cells: [{ code: "print('hi')" }], timeoutMs: 5000, cwd: tempDir.path, reset: true },
 			undefined,
 			undefined,
 			undefined,
@@ -51,7 +51,7 @@ describe("python tool execution", () => {
 			expect.objectContaining({
 				cwd: tempDir.path,
 				timeoutMs: 5000,
-				sessionId: `session:session-file:workdir:${tempDir.path}`,
+				sessionId: `session:session-file:cwd:${tempDir.path}`,
 				kernelMode: "per-call",
 				reset: true,
 			}),