Improve Extract and Publish log readability

## Summary

Feedback on the integration test logs (`tests/integration/all-resource-types/basicv2-test.log`) identified several readability and usability improvements for the Extract and Publish command output.

## Proposed Improvements

### Extract Command (`src/cli/extract-command.ts`)

1. **Group resources by dependency tier** — The "Extracted N Type(s)" lines are a flat list with no visual hierarchy. Group by tier or add blank lines between categories.

2. **List all APIs in the detail section** — Currently only APIs with specs/operations are shown (7 of 12). APIs like `src-graphql-synthetic` and `src-a2a-weather-agent` are silently omitted. List all APIs even if minimal.

3. **Add elapsed time to the Total line** — `Total: 96 resources extracted, 0 errors` should include duration (e.g., `in 12.3s`).

### Publish Command (`src/services/publish-service.ts`, `src/cli/publish-command.ts`)

4. **Add tier/phase headers** — All PUTs are a single flat stream. Since publish executes in dependency tiers, add headers:
```
── Tier 1: Independent resources (16) ──
PUT namedvalue/src-nv-plain
...
── Tier 2: Resources with dependencies (2) ──
PUT backend/src-backend-pool
```

5. **Add elapsed time** — No indication of how long publish took or which resources were slow. Add per-tier or total timing.

6. **Enrich the summary** — `41 creates/updates, 0 deletes, 1 skipped` could also show total elapsed time and retry count (e.g., "6 retries across 2 resources").

### Retry Logging (`src/clients/apim-client.ts`)

7. **Round retry delay values** — `retrying after 1175.1730686888397ms` → `retrying in 1.2s`

8. **Include resource context in retry warnings** — Currently no indication of *which* resource triggered the retry.

9. **Include attempt number** — e.g., `(attempt 2/5)` so readers know retry progress.

10. **Reduce retry noise in output** — Retries interleave with PUT lines and break the flow. Consider grouping retries under their resource or suppressing intermediate retries (show only final outcome with retry count).

## Files to Modify

- `src/cli/extract-command.ts` — items 1–3
- `src/services/publish-service.ts` — items 4–6
- `src/cli/publish-command.ts` — items 5–6
- `src/clients/apim-client.ts` — items 7–10

## Related

Based on review of `tests/integration/all-resource-types/basicv2-test.log`

まず tests/integration/all-resource-types/basicv2-test.log から始め、次に src/cli/extract-command.ts、src/services/publish-service.ts、src/cli/publish-command.ts、src/clients/apim-client.ts 内の関連する出力パスを比較します。抽出、公開、リトライが現在どのように処理内容をログに記録しているかを追跡します。出力が、API を漏らすことなく、提案されたグループ化、タイミング、サマリー、リトライコンテキストの改善を網羅していれば完了です。

索引モデルが issue の本文から書いたものです。