reduce memory usage in filtering and smoothing functions

[jrnold]

This may require reimplementing the smoothers and/or simulations

[jrnold]

For each of the filtering, smoothing, and simulation functions with more than one return value, include flags to indicate which vectors and matrices to save. This will dramatically reduce the amount of

• adding flag args to each function
• altering the index calculation and vector size functions to account for the flags
• altering the functions to conditionally save values
• altering the get functions to conditionally extract values