Fix layered graph generator not connecting all generated nodes

[uber-mahyar2]

We connect to lower layer modules at random, choosing a small subset of modules to depend on (something like 5 / 100). As a result, the more modules there are in a layered graph, the more likely there are modules that would not be be connected to the main app graph since the amount of lower level modules that are connected to by higher level modules stays constant at 5 modules.

As a result %10-%20 of modules in most graphs are not connected to the main graph. Modules not connected to the main graph are not built by most build systems, so it looks like the layered graph is inherently faster than a flat graph, while it's only compiling %10-%20 less code & modules than a flat graph.