Updated setup vignette

Author: VisruthSK

_pkgdown.yml

@@ -1,5 +1,7 @@
 url: https://mc-stan.org/pkgdown-config
+
 template:
   package: pkgdownconfig
+
 development:
   mode: auto

vignettes/Setup.qmd

@@ -10,6 +10,8 @@ knitr:
     comment: '#>'
 ---
 
+## General Setup
+
 If you haven't started a `pkgdown` site yet, initialize it.
 
 ```r
@@ -23,6 +25,15 @@ template:
   package: pkgdownconfig
 ```
 
+Optional but highly recommended is to set development mode to auto and to build the site in root, like so:
+
+```yaml
+destination: "."
+
+development:
+  mode: auto
+```
+
 Point to this repository in `DESCRIPTION` to download the theme automatically.
 
 ```yaml
@@ -83,12 +94,59 @@ navbar:
         - text: shinystan
           href: https://mc-stan.org/shinystan
 ```
+## Example (`shinystan`)
+
+Put together, here's what a reasonable YAML looks like (truncated, taken from `shinystan`):
+
+```yaml
+url: https://mc-stan.org/shinystan
+
+destination: "."
+
+development:
+  mode: auto
+
+template:
+  package: pkgdownconfig
+
+navbar:
+  title: "shinystan"
+
+  structure:
+    left: [home, vignettes, functions, news, pkgs, stan]
+    right: [search, bluesky, forum, github, lightswitch]
+
+  components:
+    pkgs:
+      text: Other Packages
+      menu:
+        - text: bayesplot
+          href: https://mc-stan.org/bayesplot
+        - text: cmdstanr
+          href: https://mc-stan.org/cmdstanr
+        - text: "loo"
+          href: https://mc-stan.org/loo
+        - text: posterior
+          href: https://mc-stan.org/posterior
+        - text: projpred
+          href: https://mc-stan.org/projpred
+        - text: rstan
+          href: https://mc-stan.org/rstan
+        - text: rstanarm
+          href: https://mc-stan.org/rstanarm
+        - text: rstantools
+          href: https://mc-stan.org/rstantools
+
+# now you can add articles, references, etc.
+```
+
+## Common Issues
 
-If for some reason the favicons don't get copied over, download [logo.svg](https://github.com/stan-dev/logos/blob/master/logo.svg), and run `pkgdown::build_favicons()` once to build the favicons. If you already have favicons, the template my overwrite them to save a copy and ping `@Visruth` on the Stan Slack.
+If for some reason the favicons don't get copied over, check if you are defining favicons in `pkgdown/favicons`. In most cases you can delete everything in that folder--just delete the logo and favicons if you are worried. The template will hook in the correct favicon and logo. If its not working, download [logo.svg](https://github.com/stan-dev/logos/blob/master/logo.svg) to `/man/figures/logo.svg` and run `pkgdown::build_favicons()` once to build the favicons.
 
-Note that the favicons and logo should be copied into your build directory and ideally should be hooked in automatically. If you can't find the logo, you can download it from [here](https://github.com/stan-dev/logos/blob/master/hex_stickers/stan_hex_cut.svg) and follow the same steps above.
+<!-- Note that logo should also be copied into your build directory and will be hooked in automatically. If you can't find the logo, you can download it from [here](https://github.com/stan-dev/logos/blob/master/hex_stickers/stan_hex_cut.svg) and follow the same steps above. -->
 
-If you want the hex in your README, edit the `README.MD`. You can take a look at this package's to get an idea of what you need to do (repeated below):
+If you want the hex in your README (or if it isn't working), make sure to edit the `README.MD` or however you generate it. You can take a look at this package's to get an idea of what you need to do (repeated below):
 
 ```md
 # pkgdownConfig <a href="https://mc-stan.org/pkgdown-config"><img src="man/figures/logo.svg" align="right" height="139" alt="pkgdownConfig website" /></a>