chore: minor cleanups — docs index, test-project fixture, empty catches, triage timestamp guard

- Add diagnostics.md and FN-4886/FN-5048 entries to docs/README.md index
- Fix test-project.test.ts spy target (updateSettings → init) to match fixture flow
- Remove unused DEFAULT_PROJECT_SETTINGS import and skip empty settings patch
- Add explanatory comments to empty catch blocks in secrets-env-writer
- Refine near-duplicate timestamp guard in triage for cleaner NaN handling

packages/core/src/__tests__/test-project.test.ts

@@ -136,7 +136,7 @@ describe("test-project fixture", () => {
     const projectCountBefore = countTmpDirs(projectPrefix);
     const globalCountBefore = countTmpDirs(globalPrefix);
     const error = new Error("boom");
-    const spy = vi.spyOn(TaskStore.prototype, "updateSettings").mockRejectedValueOnce(error);
+    const spy = vi.spyOn(TaskStore.prototype, "init").mockRejectedValueOnce(error);
 
     try {
       await expect(

packages/core/src/__tests__/test-project.ts

@@ -5,7 +5,6 @@ import { isAbsolute, join } from "node:path";
 
 import { TaskStore } from "../store.js";
 import {
-  DEFAULT_PROJECT_SETTINGS,
   GLOBAL_SETTINGS_KEYS,
   type GlobalSettings,
   type Settings,
@@ -42,7 +41,7 @@ function splitSettings(settings?: Partial<Settings>): {
   projectPatch: Partial<Settings>;
 } {
   const globalPatch: Partial<GlobalSettings> = {};
-  const projectPatch: Partial<Settings> = { ...DEFAULT_PROJECT_SETTINGS };
+  const projectPatch: Partial<Settings> = {};
 
   for (const [key, value] of Object.entries(settings ?? {})) {
     if (isGlobalSettingsKey(key)) {
@@ -89,7 +88,9 @@ export async function createTestProject(
     await store.init();
 
     const { globalPatch, projectPatch } = splitSettings(options.settings);
-    await store.updateSettings(projectPatch);
+    if (Object.keys(projectPatch).length > 0) {
+      await store.updateSettings(projectPatch);
+    }
 
     if (Object.keys(globalPatch).length > 0) {
       await store.updateGlobalSettings(globalPatch);