Fix Setup Types

Setup Types need to be corrected so that:
- Panels and Commands should be keyed by string values (e.g. the id)
- All methods are optional
- menuItems has all optional parameters
- Additionally argument types need to be specified.

Here is an example of what it should look like:

```ts
setup(entrypoints: {
plugin?: {
create?: (...params: any[]) => any;
destroy?: (...params: any[]) => any;
};
panels?: {
[key:string]:{
create?: (rootNode: HTMLElement) => any;
show?: (rootNode: HTMLElement, data: any) => any;
hide?: (rootNode: HTMLElement, data: any) => any;
destroy?: (rootNode: HTMLElement) => any;
invokeMenu?: (id: string) => any;
customEntrypoint?: (...params: any[]) => any;
menuItems?: {
id: string;
label: string;
enabled?: boolean;
checked?: boolean;
submenu?: any[];
}[];
};
};
commands?: {
[key:string]:{
run: (...params: any[]) => any;
cancel?: (...params: any[]) => any;
};
};
}): void;
```

Start by locating the TypeScript declaration for the setup entrypoint and inspect the existing Panels, Commands, and menuItems types. Update the declarations to match the example: string-keyed entries, optional methods and menu parameters, and specified argument types; done means the setup signature matches these requirements and type-checks.

Written by the indexing model from the issue text.