Fixes to fire mortality diagnostics, patch disturbance area checks and trimming

This release adds a modest set of feature changes and several small bug fixes. The small feature additions improve the way that mortality is calculated for fire, by saving these diagnostics to a tracking array. The bug fixes are as follows: 1) Many site level diagnostics were not being saved in restarts, thereby the first day following a restart was contributing bogus information to the diagnostics, 2) the net assimilation budget had not been correctly calculating night-time respiration for trimming calculations (the prognostic carbon balance was not affected) , and 3) in very rare cases, patches with nearly zero sizes were creating problems during patch generation and creating problems during carbon balance checks, so checks were implemented. Contributions from Jackie Shuman, Charlie Koven, Ryan Knox, and others.