Update vignettes

[kellijohnson-NOAA]

Problem

The vignettes hadn't been looked at in a while and a large number of issues with the vignette label were accumulating. Also, pkgdown is pretty great and will add to the user experience.

Proposal

• use nmfs-fish-tools pkgdown template #333
• Move detailed information in Information vignette to function documentation #330
• change_tv() should be able to add tv parameters when there are none #329
• misleading line in vignette about change_tv column #315
• update self testing section of vignette #307
• Update the figure on Readme of input/output file structure #292
• Add set of examples using ss3sim #277
• Create more issues to document things that you see when working on the above issues

Disclaimers

• there is the potential for not all of the issues to be closed in the vignette branch, which is okay, just remove the working on label and save them for a later date

[k-doering-NOAA]

It would be nice to include in the vignette an example of specifying om and em directories within the sim df; For example, https://github.com/k-doering-NOAA/cal-sims/blob/ce4ada6df484e8b941d81227e7e4419f051569ad/code/piner_et_al_scenarios.R#L89-L90

However, it would be even more helpful to show different om/em paths per scenario