check knitr options

[richfitz]

Wrong, but no warning:

  MS/SuppMatt.md:
    knitr: 
      options: 
        auto_figure_prefix: true
        chdir: true

intended

  MS/SuppMatt.md:
    knitr: 
      auto_figure_prefix: true
      chdir: true

docs need clearing up https://github.com/richfitz/remake/blob/master/doc/format.md#knitr-targets

@aammd

[wlandau]

Did you end up deciding on the first one? I noticed that the first one works as expected, but the second one throws a warning and ignores the knitr options. workflowHelper currently assumes the former.