A powerful idea that from my knowledge would be pretty simple to implement- in MechJebCore.cs, where the ComputerModule list is populated, instead of hardcoding the entries, use reflection to find all types that extend from ComputerModule and create them using C#'s Activator class.
For example, the following line of code does this (replace all the "modules.Add"s with this)
modules = AppDomain.CurrentDomain.GetAssemblies().SelectMany(assembly => assembly.GetTypes()).Where(type => type.BaseType == typeof(ComputerModule)).Select(type => Activator.CreateInstance(type, this)).OfType().ToList();
Basically, this allows people like myself to take advantage of the (quite awesome) already-existing framework of Mechjeb without forking it. It also allows the user to install more than one mechjeb mod.