fix timing of generate_quantities

[avehtari]

Summary

Closes #1070. generate_quantities did not update timing information. This PR adds the timing information.

Copyright and Licensing

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Aki Vehtari

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/)

[jgabry]

Looks like this causes some failures in the existing timing tests

[avehtari]

My bad, I forgot to run all tests. Now fixed, and I'll add more details.
Also I'm fine if this is not merged and we fix this in CmdStan

[codecov-commenter]

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 86.97%. Comparing base (453084b) to head (e235690).
⚠️ Report is 16 commits behind head on master.

Additional details and impacted files

@@            Coverage Diff             @@
##           master    #1141      +/-   ##
==========================================
- Coverage   87.49%   86.97%   -0.53%     
==========================================
  Files          14       14              
  Lines        5983     5941      -42     
==========================================
- Hits         5235     5167      -68     
- Misses        748      774      +26     

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[avehtari]

I'm closing this as this is better to fix in stan services so that the timing information is written in csv