Restructure inputs

[geraintpalmer]

Huge changes to the way parameters are input into the system::

• Simulation objects now takes in a Network object
• helper functions to create Network object from dictionary / yml file
• rearrange server schedules so no need to define Cycle_length
• simulate_until_max_time takes in max_simulation_time argument
• Simulation object takes deadlock_detector, exact, and state_tracker arguments along with Network object

[coveralls]

Coverage remained the same at 100.0% when pulling 11fed47 on restructure-inputs into 2d47ffa on master.