refactor: simplify plugin dependency handling

Simplify plugin installation and runtime loading around package-manager-owned dependencies, with Jiti reserved for local/TS fallback paths.

Also scans npm plugin install roots so hoisted transitive dependencies are covered by dependency denylist and node_modules symlink checks.

extensions/matrix/package.json

@@ -80,9 +80,6 @@
       "defaultChoice": "npm",
       "minHostVersion": ">=2026.4.10",
       "allowInvalidConfigRecovery": true
-    },
-    "bundle": {
-      "stageRuntimeDependencies": true
     }
   }
 }