fix(review): skip RAG pruning for truncated trees

[VitoBeijing]

Summary

• surface the GitHub recursive-tree truncated flag to RAG indexing
• skip destructive missing-path pruning when the returned tree is incomplete
• continue indexing returned entries and preserve complete-tree pruning behavior
• add regression coverage for both complete and truncated trees
• freeze the gate-outcome dashboard test clock so its fixed audit fixtures remain inside the tested 30-day window

Closes #10328

Validation

• git diff --check
• npm run actionlint
• npm run typecheck
• npx vitest run test/unit/rag-index.test.ts — 53 passed
• npx vitest run test/unit/routes-gate-outcome-breakdown.test.ts — 6 passed
• npm run test:workers
• npm run build:mcp
• npm run test:mcp-pack
• npm run ui:openapi:check
• npm run ui:lint
• npm run ui:typecheck
• npm run ui:build

Full-suite note: 26,765 tests passed; 41 concurrent tests timed out locally.
The affected Git fixture suite passed 79/79 when run in isolation with the
user-level Git hook configuration excluded.

Notes

The dashboard test fix only controls Date and restores real timers after each test.
No production dashboard behavior, UI, API contract, dependency, authentication,
or authorization changes.

[superagent-security]

Superagent didn't find any vulnerabilities or security issues in this PR.

[codecov]

❌ 2 Tests Failed:

Tests completed	Failed	Passed	Skipped
4912	2	4910	11

View the top 2 failed test(s) by shortest run time

test/unit/routes-gate-outcome-breakdown.test.ts > GET /v1/app/maintainer-dashboard gateOutcomeBreakdown (#2203) > excludes non-terminal and non-gate audit rows from gateOutcomeBreakdown totals

Stack Traces | 0.164s run time

AssertionError: expected { windowDays: 30, …(5) } to match object { total: 1, counts: { …(3) } }
(7 matching properties omitted from actual)

- Expected
+ Received

  {
    "counts": {
      "autoClosed": 0,
-     "autoMerged": 1,
+     "autoMerged": 0,
      "held": 0,
    },
-   "total": 1,
+   "total": 0,
  }

 ❯ test/unit/routes-gate-outcome-breakdown.test.ts:147:56

test/unit/routes-gate-outcome-breakdown.test.ts > GET /v1/app/maintainer-dashboard gateOutcomeBreakdown (#2203) > surfaces repo-scoped gate-outcome counts on qualityDashboard for an owner session

Stack Traces | 0.337s run time

AssertionError: expected { windowDays: 30, …(5) } to match object { windowDays: 30, total: 3, …(2) }
(2 matching properties omitted from actual)

- Expected
+ Received

  {
    "counts": {
-     "autoClosed": 1,
-     "autoMerged": 1,
-     "held": 1,
+     "autoClosed": 0,
+     "autoMerged": 0,
+     "held": 0,
    },
    "rates": {
-     "autoClosed": 33.3,
-     "autoMerged": 33.3,
-     "held": 33.3,
+     "autoClosed": null,
+     "autoMerged": null,
+     "held": null,
    },
-   "total": 3,
+   "total": 0,
    "windowDays": 30,
  }

 ❯ test/unit/routes-gate-outcome-breakdown.test.ts:79:56

To view more test analytics, go to the Test Analytics Dashboard
_{📋 Got 3 mins? Take this short survey to help us improve Test Analytics.}