Docs update from dec/jan changes

[bwhitman]

We made a lot of very great changes to AMY over the past few months. The docs did not get as much love as the code did. There's a lot of missing pieces in the docs and the tutorials could use a look over again.

[bwhitman]

One big thing people are running into is the amp_coefs, vs amp, freq_coefs vs freq, etc. In python we do amp=X or amp=X,Y,Z and it doesn't translate into C events.