feat: 诊断（任务书 18 第一块）：诊断数学、四种提交、一次运行跑多个实验、账本与材料、flow 诊断各步

消融默认关，关掉时解释阶段一并跳过；选诊断实验用信息价值减成本。
eval/diagnosis/research.json 为第三块配置。vocab 字段说明的出口文字随提示词一起改，见下一次提交的 prompts/ 与同文件改动（本次含在内）。

Co-Authored-By: Claude Sonnet 5.5 <noreply@anthropic.com>

tests/workspace.test.ts

@@ -260,3 +260,23 @@ test("比较的行号：改一行、加几行、只删不加，新旧两边的
   // 给模型看的差异原文带 3 行上下文：三处改动相隔不到 6 行，合成一块。
   assert.match(result.diff, /^@@ -1,10 \+1,12 @@\n a\n-b\n\+B\n c\n d\n e\n\+X\n\+Y\n\+Z\n f\n g\n-h\n i\n j\n$/m);
 });
+
+test("诊断程序（任务书 18）：基线代码取出后放进只读的原始产物、改成诊断程序再存，产物被跳过，比较只看程序的改动，取出再存号不变", (t) => {
+  const repo = newRepo(t);
+  const baseline = save(repo, makeDir(t, { "initial.py": "a\nb\n", "evaluate.py": "e\n" }), []);
+  const workDir = checkout(t, repo, baseline);
+  // 原始产物放进实验员工作目录，设成只读（0444），与 tasks 的 placeBaselineArtifact 一样。
+  mkdirSync(join(workDir, "baseline-artifact"));
+  writeFileSync(join(workDir, "baseline-artifact", "solution.json"), "{}");
+  chmodSync(join(workDir, "baseline-artifact", "solution.json"), 0o444);
+  writeFileSync(join(workDir, "initial.py"), "a\nb\nexperiment\n");
+  const excluded = ["__pycache__", "solution.json", "baseline-artifact"];
+  const program = save(repo, workDir, excluded);
+  assert.notEqual(program, baseline);
+  const comparison = compareVersions(repo, baseline, program);
+  assert.deepEqual(comparison.files.map((f) => f.path), ["initial.py"]);
+  assert.deepEqual((comparison.files[0] as Extract<FileChange, { binary: false }>).hunks, [{ from: { after: 2 }, to: { start: 3, end: 3 } }]);
+  const again = checkout(t, repo, program);
+  assert.equal(existsSync(join(again, "baseline-artifact")), false);
+  assert.equal(save(repo, again, excluded), program);
+});