Fix several bugs related to estimated measurement errors

1. The first call to set_prior overwrote the first column of
estim_params_.var_endo storing the position of the variable with
measurement error in M_.endo_names with the position in
options_.var_obs. All subsequent calls to set_prior then lead to
crashes.
2. At the same time, for correlations of ME, the first column of
estim_params_.corrn still stored the position of the variable with
measurement error in M_.endo_names. But subsequent calls to it were done
as if it stored the position in options_.var_obs

I introduced two new variables in estim_params_ storing the respective
positions in var_obs so as to not necessitate changes in the
preprocessors.

3. For cases of calibrated measurement error correlations, the
covariance matrix was not updated.

4. Fixing a lot of smaller bugs related to measurement errors, including
some copy and paste errors
-
(cherry picked from commit 7518072e7762c54e39d75c2f6e1e6261f416efa4)
Add unit test for correlated measurement error

Tests both ML and Bayesian estimation and test calibrated correlation of
those shocks
(cherry picked from commit 0311c4add48a81af7b01ca91dbdc9909669b1688)
Clarify treatment of measurement error and correlations in manual
(cherry picked from commit 34fb9f1c62c63e7e4ab41656a7690167449e596f)
Fix bug in ML forecasting if observables are not included
(cherry picked from commit 156397ec319ac9f907b775020dd5001b4b29830a)
Incorporate unit test for correlation in measurement errors
(manually cherry picked from commit 214ff84429ad2c28391c5ce5ea4d3bc771078e09)