Make constrain_pars behaviour consistent with rstan

[andrjohns]

Submission Checklist

• Run unit tests
• Declare copyright holder and agree to license (see below)

Summary

The constrain_pars method in RStan also returns the transformed parameters and generated quantities implied by the provided unconstrained parameters. This PR adds two boolean arguments to the cmdstanr constrain_pars for whether to return the transformed parameters and/or generated quantities (defaulting to TRUE for consistency with rstan):

fit$constrain_pars(c(0.1))
#> $theta
#> [1] 0.5249792
#> 
#> $log_lik
#>  [1] -7.243967 -7.243967 -7.243967 -7.243967 -7.243967 -7.243967 -7.243967
#>  [8] -7.243967 -7.243967 -7.243967

fit$constrain_pars(c(0.1), generated_quantities = FALSE)
#> $theta
#> [1] 0.5249792

^{Created on 2022-10-16 with reprex v2.0.2}

Copyright and Licensing

Please list the copyright holder for the work you are submitting
(this will be you or your assignee, such as a university or company):
Andrew Johnson

By submitting this pull request, the copyright holder is agreeing to
license the submitted work under the following licenses:

• Code: BSD 3-clause (https://opensource.org/licenses/BSD-3-Clause)
• Documentation: CC-BY 4.0 (https://creativecommons.org/licenses/by/4.0/)

[codecov-commenter]

Codecov Report

Merging #704 (4ecfd85) into master (cdd62a0) will increase coverage by 1.06%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #704      +/-   ##
==========================================
+ Coverage   89.48%   90.55%   +1.06%     
==========================================
  Files          12       12              
  Lines        3824     3884      +60     
==========================================
+ Hits         3422     3517      +95     
+ Misses        402      367      -35     

Impacted Files	Coverage Δ
R/fit.R	98.22% <100.00%> (+<0.01%)	⬆️
R/utils.R	86.35% <100.00%> (+0.99%)	⬆️
R/csv.R	97.66% <0.00%> (+0.42%)	⬆️
R/model.R	91.71% <0.00%> (+0.98%)	⬆️
R/run.R	95.28% <0.00%> (+1.57%)	⬆️
R/install.R	62.93% <0.00%> (+4.19%)	⬆️

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