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

peptide-search-ai.php

@@ -3,7 +3,7 @@
  * Plugin Name: Peptide Search AI
  * Plugin URI:  https://github.com/peptiderepo/peptide-search-ai
  * Description: Searchable peptide database with AI-powered auto-population and browsable directory.
- * Version:     4.6.0
+ * Version:     4.7.0
  * Author:      peptiderepo
  * License:     GPL v2 or later
  * Text Domain: peptide-search-ai
@@ -15,7 +15,7 @@ if ( ! defined( 'ABSPATH' ) ) {
 	exit;
 }
 
-define( 'PSA_VERSION', '4.5.0' );
+define( 'PSA_VERSION', '4.7.0' );
 define( 'PSA_PLUGIN_DIR', plugin_dir_path( __FILE__ ) );
 define( 'PSA_PLUGIN_URL', plugin_dir_url( __FILE__ ) );
 define( 'PSA_PLUGIN_FILE', __FILE__ );