ci: adopt reusable CI + 300-line compliance for v4.7.0

- Replace per-repo CI jobs with thin reusable caller
  (peptide-e2e ci.yml@main; tests:stubs, has_js:true)
- Add permissions: contents: write (required for phpcbf auto-commit)
- deploy.yml: drop file-existence + PHP-syntax redundancy; keep PSA_VERSION check
- class-psa-admin.php: remove 37 dead backward-compat proxy lines (327→290)
- class-psa-ai-generator.php: remove 17 dead backward-compat proxy lines (309→292)
- class-psa-search.php: remove 13 dead backward-compat proxy lines (307→294)
  All three files now comply with the estate 300-line rule.
  Zero external callers of removed methods confirmed.
- package.json / package-lock.json: minimal npm manifest for lint-js npm ci step
- ARCHITECTURE.md: update ci.yml description
- PSA_VERSION: sync constant (was 4.5.0) with header (was 4.6.0) → both 4.7.0

Agent-Session: claude-sonnet-4-6-adopt-ci-20260616

ARCHITECTURE.md

@@ -43,7 +43,7 @@ peptide-search-ai/
 │       └── psa-directory.css          Directory card grid, filter pills, modal styles, dark mode support
 │
 └── .github/workflows/
-    ├── ci.yml                         PHP lint, PHPCS, JS syntax checks on PR/push
+    ├── ci.yml                         Thin caller → peptide-e2e reusable CI (stubs, has_js:true); blocking PHPCS + 300-line rule
     └── deploy.yml                     Pre-deploy validation, orphan deploy branch sync, SSH deploy
 ```