joobei

string jsondata = File.ReadAllText(Application.dataPath + "/../" + fileName + ".json");
Debug.Log (jsondata);
Connection[] temparray = new Connection[JsonHelper.FromJson<Connection>(jsondata).Length];
                                        ^---- This is where it breaks. 
Debug.Log (temparray.Length);

foreach (Connection connection in JsonHelper.FromJson<Connection>(jsondata)) 
{
  connections.Add (connection);
}

joobei

public static class Util
{
    public static Vector3[,] generatePositions(List<int> angles, List<float> depths)
    {
        Vector3[,] positions = new Vector3[angles.Count,depths.Count];
                                           ^            ^      
        NullReferenceException: Object reference not set to an instance of an object
        Util.generatePositions (System.Collections.Generic.List`1 angles, System.Collections.Generic.List`1 depths) (at Assets/Scripts/Util.cs:29)
        DockingState..ctor () (at Assets/Scripts/States/DockingState.cs:32)

joobei

class State: Monobehaviour {
  
  //reference to the state we will need to jump to
  public State nextState;
  
  protected virtual void Update()
  {
    if (mouseClicked) 
	{ 
		doSomething();