Refactor kinematics functions and associated ODE functions

• Split sensitivity calculation into their own functions
  • Sensitivities will, for now, be put on hold
• Move kinematics ODEs into ode.kinematics subpackage
• Move sensitivity ODEs into ode.sensitivity subpackage
  • Sensitivities will, for now, be put on hold
• Move variation ODEs into ode.variation subacpkage

This closes #1 (closed), #4 (closed), and #5 (closed)