Bugfixes for correlated shocks

Uses preprocessing capabilities introduced in 07137e804b34a0e615398cb7cb5876f4a9027274

Fixes #392 and #494. Also fixes a bug in the checking for positive definiteness of covariance matrices in dsge_likelihood.m

Allows for calibrated covariances by reading them out and setting them after covariance matrix has been reconstructed from correlation and variances.

Adds unit test