add support for case 2 and case 3 connection between spiking ensembles

- ref #52
- handles the connections in test_decoded_weight_matrix
- the 2 new connections apply the transformation matrix differently
- socket names are unique across decoded and incoded inputs
- ensemble can distinguish between an incoded and a decoded input connection
add and update comments
Merge pull request #54 from Hudon/special-connections

Special connections