Commit prior to trying to add fixed and linear trend effects to RW2 models.  Thought is that putting informative priors on these should tighten up estimates and prevent REs from blowing up.  This change was prompted by beginning some Bering Sea simulations where effort was missing for certain days and STPC results were full of NAs and sometimes really large.

In addition to first commits for Bering sea simulation code, the following changes were implemented and/or bugs fixed:

-'chol' now used instead of 'Cholesky' in mcmc_STPC... much more stable
-In simulation scripts, output file didn't specify generating model
-Data$Which.distances was wrong for "RS2open" sims.
-Added Area.adjust to simulation functions
-Fixed bug in initial dimension of "Accept" in mcmc_STPC.R and mcmc_AST.R that generated warnings
-Removed dependence on DoBy package when calculating C_t in preamble of mcmc_CPIF.R (resulted in error when missing effort at some time steps)
-Now order count data in mcmc_CPIF in preamble to enable better switching between list, vector formats
-Added a small diagonal element to prior precision matrix in RW2 updates (helps ensure invertibility)
-For AST, specified all time steps as factors in Tmp.dat when setting up RW2 model (issue when missing effort at certain times)