fix: correct query .set and .refresh behavior in commands

[phi-bre]

Closes #14832
Closes #14602

• A query can now be called more than once in a single command and calling .refresh() will re-run the remote function (which IMO is the expected behavior when comparing it to client side .refresh functionality)

  export const getTodos = query(async () => {
    // returns todo list from database
  });
  
  export const addTodo = command(async () => {
    const previousTodos = await getTodos();
  
    // Do something that depends on existing todos
  
    await getTodos().refresh(); // Rerun the query so the data sent via single flight mutation is up to date   
  });

• Calling await getTodos().refresh() only once in the command will not trigger the function twice (unchanged from current behavior)
• Adds missing query.batch .set operation that was supposed to exist based on existing typescript types but didn't.
• At the same time, this PR should prevent non-exported query functions from writing to the refreshes cache but still update the function cache correctly.

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