fix: rm deprecated class modules, clean up, rm indirection (#355)

* refactor: rm deprecations, clean up, rm indirection

* fix: singleton init not being fired when inserting function

* refactor and generic internal add

* deprecate a few things that i impusively added lol

src/core/structures/module-store.ts

@@ -7,5 +7,5 @@ import { CommandMeta, Module } from '../../types/core-modules';
  */
 export class ModuleStore {
     metadata = new WeakMap<Module, CommandMeta>();
-    commands = new Map<string, string>();
+    commands = new Map<string, Module>();
 }