Issue/870 affine xform clarification

[mitzimorris]

Submission Checklist

• [x] Builds locally
• [x] New functions marked with <<{ since VERSION }>>
• [x] Declare copyright holder and open-source license: see below

Summary

Minor clarifications to Reference Manual on affine transform, added example of Neal's funnel using affine xform to Stan User's Guide chapter on efficiency tuning.

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): Columbia University

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