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Documentation for the Stan language and CmdStan

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We should have `num_threads` more thoroughly documented, especially for other interfaces. It also seems like the cmdstan example calls are wrapping over the lines in the PDFs

#### Summary: Update all of our docs as to where `target +=` and `XXX_lp` functions can be used. #### Description See https://github.com/stan-dev/stanc3/issues/979 #### Current Version: v2.18.0

enhancement

#### Summary: Model description uses y for output variables but Stan code uses `w`. #### Description: https://mc-stan.org/docs/2_27/stan-users-guide/hmms-section.html #### Additional Information: N/A #### Current Version: v2.18.0

#### Summary: Add a chapter to the *Stan User's Guide* on refactoring programs for clarity. #### Description: We essentially want to port the non-OO parts of Martin Fowler's book, *Refactoring*....

enhancement

#### Summary: We currently do not test whether the changes in a PR produce valid syntax. This causes minor issues at release time when we regenerate the html and PDF...

The "[Space before includes](https://mc-stan.org/docs/2_26/reference-manual/includes-section.html#space-before-includes)" section says: > It is possible to use includes on a line non-initially. then immediately thereafter: > If there is initial space before an include, it...

Following up on https://discourse.mc-stan.org/t/issues-with-e-bfmi-missing-doc-confusing-name-etc/22553. E-BFMI is not documented anywhere (at least using the search functionality in the user's guide and reference manual there were no results for "BFMI"). The only...

When `V` is a vector sequential processing is used. This should be explicit in the first paragraph. Right now it just says that a more effecient processing can be used...

I believe this is a docs issue with the normal distribution. The documentation at https://mc-stan.org/docs/2_26/functions-reference/normal-distribution.html#normal-distribution says that `Phi_approx` is more robust in the tails. However, inspecting this shows that using...

#### Summary: The reduce_sum documentation is incomplete. It does not briefly mention how things should be done to really gain performance. For example that shared arguments are copied if they...