Add network config option to save GTFS shapes

[ansoncfit]

Fixes #751

[trevorgerhardt]

Changes look good to me. Do we know why those tests are failing? Once we address those I will approve.

[abyrd]

After discussing with Anson I made some changes. The reason the network was changing after deserialization was that some of its fields were not being initialized. This is because the default (no-arg) constructor no longer existed so the deserialization was using a special non-constructor approach to instantiate the object, which leaves those fields null instead of evaluating their initialization expressions. The underlying reason is a Java quirk: default no-arg constructors exist automatically until you add some other constructor with arguments, then the default one is no longer created automatically.