Bugfix - Deep copy method/function environments

[andrjohns]

Submission Checklist

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

Summary

There was a bug with the model methods and exposed functions wherein running init_model_methods() on a CmdStanFit object would overwrite the model methods from all CmdStanFit objects that came from the same CmdStanModel.

This was because the environment was being passed by reference from the CmdStanModel object when initialising each CmdStanFit, so every fit object was pointing to the same environment.

This PR updates the initialisation to create a new environment and copy the contents, as well as adding a test to check for this in the future

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/)

[rok-cesnovar]

Thanks! Merge once you get the unit tests to pass.

[codecov-commenter]

Codecov Report

Merging #709 (6d0105b) into master (f8f6321) will increase coverage by 0.01%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #709      +/-   ##
==========================================
+ Coverage   88.44%   88.46%   +0.01%     
==========================================
  Files          12       12              
  Lines        4017     4021       +4     
==========================================
+ Hits         3553     3557       +4     
  Misses        464      464              

Impacted Files	Coverage Δ
R/fit.R	97.47% <100.00%> (+0.03%)	⬆️
R/utils.R	73.40% <100.00%> (-0.12%)	⬇️

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