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.

src/cli/program/preaction.test.ts

@@ -245,7 +245,6 @@ describe("registerPreActionHooks", () => {
     });
     expect(ensurePluginRegistryLoadedMock).toHaveBeenCalledWith({
       scope: "all",
-      installBundledRuntimeDeps: true,
     });
   });
 
@@ -262,7 +261,6 @@ describe("registerPreActionHooks", () => {
     });
     expect(ensurePluginRegistryLoadedMock).toHaveBeenCalledWith({
       scope: "all",
-      installBundledRuntimeDeps: true,
     });
   });