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

package-lock.json

@@ -0,0 +1,13 @@
+{
+  "name": "peptide-search-ai",
+  "version": "4.7.0",
+  "lockfileVersion": 3,
+  "requires": true,
+  "packages": {
+    "": {
+      "name": "peptide-search-ai",
+      "version": "4.7.0",
+      "devDependencies": {}
+    }
+  }
+}