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Dynare (no function calls it).

*  Removed the  necessity (for  the  user) to  run stoch_simul  bebore
executing the exetended path routine (when options_.init>0).

*  The  value  of  options_.ep.init  defines the  mix  (used  for  the
initialization of  the perfect foresight solver)  between the previous
perfect foresight  solution and  the path obtained  with an  order one
perturbation approach.

* Removed timing related statements.

*  Changed homotopy set-up  for stochastic  extended path:  add future
multivariate innovations one by one.

* Endogeneously increase step_length in the homotopy routine.

* Removed homotopy_2 related code.

Prevent homotopy routine to enter in the second loop (doi not (re)start the homotopy from weight=0).

for computation of likelihood with presample

diffuse Kalman filter was used before

with correlated measurement errors

* bug fix when posterior filter or forecast are not triggered. (thanks to Daniel from the Dynare Forum)

Manual cherry pick from 4.2 commit:fdb364e4

penalty in dsge_likelihood.m and dsge_likelihood_hh.m Removed misleading
initialization code. Added call to dsge_likelihood_hh in
initial_estimation_checks to initialize persistent variable in that
function as well.

Revert "added calls to re-initialize persistent variable 'penalty' in dsge_likelihood() and dsge_likelihood_hh() before calling the optimizer"
This reverts commit 108444b7.

The initialization works indeed differently and I will document it in next commit.

Copyright Dynare Team and GFDL-1.3, with the consent of Marco Ratto

Closes: #173

Closes: #235

dsge_likelihood() and dsge_likelihood_hh() before calling the
optimizer