Disordered mechanical systems, when strongly deformed, have complex configuration spaces with multiple stable states and pathways connecting them. The topology of such pathways determines which states are smoothly accessible from any part of configuration space. Controlling this topology would allow us to limit access to undesired states and select desired behaviors in metamaterials. Here, we show that the topology of such pathways, as captured by bifurcation diagrams, can be tuned using imperfections such as stiff hinges in elastic networks and creased thin sheets. We derive Linear Programming-like equations for designing desirable pathway topologies. These ideas are applied to eliminate the exponentially many ways of misfolding self-folding sheets by making some creases stiffer than others. Our approach allows robust folding by entire classes of external folding forces. Finally, we find that the bifurcation diagram makes pathways accessible only at specific folding speeds, enabling speed-dependent selection of different folded states.