Integrate With the Recent Changes to the Main OTP Repository

[DJSekora]

Main repository located at https://github.com/openplans/opentripplanner

Much of the actual merging work has already been demonstrated at https://github.com/DJSekora/cta-otp. All that needs to be done to turn that into a functional version is:

1. Figure out how to use graph builder without graph-builder.jar, because this jar appears to have been removed for the moment
2. Incorporate any important new changes made to the main repository by OpenPlans (basically any changes made after the creation of the DJSekora/cta-otp repository
3. Update the README.md to match the one here
4. Update the wiki and README.md for the new file system. Also modify the section on Graph Builder in Terminal with instructions on how to run Graph Builder without graph-builder.jar