Question

If you look at the code its clearly defined and public.

<?php
class Config {
  public function prep_connections($collection){

  }

  public function get_connctions(){
    require_once('readfile.php');

    $reader = new Readfile();

    $collections = json_decode($reader->read("../../config/database.cfg"));

    foreach($collections as $collection){
       prep_connections($collection);
    }
  }
}

$config = new Config();
$connections = $config->get_connctions();

Answer 1

You need to call it via $this, to tell it is in the same/this class

$this->prep_connections($collection);