Add prism and code copy by default

2 files changed, 117 insertions, 89 deletions

diff --git a/README.md b/README.md
index d3c1bcc..fdf2fcd 100644
--- a/README.md
+++ b/README.md
@@ -24,7 +24,15 @@ The final layout this guide produces, relative to your document root:
 └── assets/
     ├── js/
     │   ├── docsify.min.js
-    │   └── search.min.js
+    │   ├── search.min.js
+    │   ├── docsify-copy-code.min.js
+    │   ├── prism-core.min.js
+    │   ├── prism-clike.min.js
+    │   ├── prism-javascript.min.js
+    │   ├── prism-bash.min.js
+    │   ├── prism-yaml.min.js
+    │   ├── prism-python.min.js
+    │   └── prism-r.min.js
     └── css/
         └── vue.css
 ```
@@ -70,33 +78,49 @@ Replace `vue.css` in the command above with any of the following if preferred; s
 * pure.css
 * vue.css
 
-### Optional: Syntax Highlighting
+### Syntax Highlighting (Prism)
 
-If your documentation includes fenced code blocks, download Prism and the language components you need:
+Download the Prism highlighting engine and its language components. The core engine
+ships **no languages on its own**, so each language is a separate file. Note that
+`prism-clike.min.js` is the base grammar that `prism-javascript.min.js` extends, so it
+must be downloaded and loaded **before** javascript (see Step 3).
 
 ```bash
-# Prism core (required)
+# Prism core engine (no languages on its own)
 curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-core.min.js" \
   -o assets/js/prism-core.min.js
 
-# Language components — add as many as needed
+# clike — base grammar required by javascript
+curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-clike.min.js" \
+  -o assets/js/prism-clike.min.js
+
+# Language components
+curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-javascript.min.js" \
+  -o assets/js/prism-javascript.min.js
+
 curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-bash.min.js" \
   -o assets/js/prism-bash.min.js
 
 curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-yaml.min.js" \
   -o assets/js/prism-yaml.min.js
 
-curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-javascript.min.js" \
-  -o assets/js/prism-javascript.min.js
+curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-python.min.js" \
+  -o assets/js/prism-python.min.js
+
+curl -L "https://cdn.jsdelivr.net/npm/prismjs@1/components/prism-r.min.js" \
+  -o assets/js/prism-r.min.js
 ```
 
-Then add each `<script>` tag for these files to `index.html` (see Step 3).
+To highlight more languages, download additional `prism-<lang>.min.js` files (browse the
+[Prism components](https://cdn.jsdelivr.net/npm/prismjs@1/components/)) and add a matching
+`<script>` tag in Step 3. Some languages extend others — anything built on `clike` (e.g.
+javascript) must load after `prism-clike.min.js`.
 
-### Optional: Copy-to-Clipboard Button
+### Copy-to-Clipboard Button
 
-To add a **copy** button to every fenced code block, download the
-[docsify-copy-code](https://github.com/jperasmus/docsify-copy-code) plugin. As with
-the assets above, it is fetched once and served locally thereafter:
+Add a **copy** button to every fenced code block with the
+[docsify-copy-code](https://github.com/jperasmus/docsify-copy-code) plugin. Like the
+assets above, it is fetched once and served locally thereafter:
 
 ```bash
 # Copy-to-clipboard plugin
@@ -148,15 +172,16 @@ Create `index.html`:
   </script>
   <script src="assets/js/docsify.min.js"></script>
   <script src="assets/js/search.min.js"></script>
-
-  <!-- Remove the line below if you did not download the copy-code plugin -->
   <script src="assets/js/docsify-copy-code.min.js"></script>
 
-  <!-- Remove the lines below if you did not download Prism -->
+  <!-- Prism: core engine first, then clike (required by javascript), then languages -->
   <script src="assets/js/prism-core.min.js"></script>
+  <script src="assets/js/prism-clike.min.js"></script>
+  <script src="assets/js/prism-javascript.min.js"></script>
   <script src="assets/js/prism-bash.min.js"></script>
   <script src="assets/js/prism-yaml.min.js"></script>
-  <script src="assets/js/prism-javascript.min.js"></script>
+  <script src="assets/js/prism-python.min.js"></script>
+  <script src="assets/js/prism-r.min.js"></script>
 </body>
 </html>
 ```
@@ -257,7 +282,15 @@ Expected output:
 ./assets/css
 ./assets/css/vue.css
 ./assets/js
+./assets/js/docsify-copy-code.min.js
 ./assets/js/docsify.min.js
+./assets/js/prism-bash.min.js
+./assets/js/prism-clike.min.js
+./assets/js/prism-core.min.js
+./assets/js/prism-javascript.min.js
+./assets/js/prism-python.min.js
+./assets/js/prism-r.min.js
+./assets/js/prism-yaml.min.js
 ./assets/js/search.min.js
 ./getting-started.md
 ./index.html
@@ -310,5 +343,9 @@ curl -L "https://cdn.jsdelivr.net/npm/docsify@4.13.1/themes/vue.css" \
   -o assets/css/vue.css
 ```
 
+The Prism components (`prismjs@1`) and the copy-code plugin (`docsify-copy-code@3`)
+are versioned independently of Docsify; re-run their Step 2 commands with a pinned
+version number the same way when you want to update them.
+
 Check the [Docsify releases page](https://github.com/docsifyjs/docsify/releases)
 for the latest version number before upgrading.
diff --git a/scripts/setup.sh b/scripts/setup.sh
index ab24775..a404eae 100755
--- a/scripts/setup.sh
+++ b/scripts/setup.sh
@@ -3,38 +3,40 @@
 #
 # Run this script from your Apache document root:
 #   cd /path/to/docroot
-#   bash setup-docsify.sh [--with-prism] [--with-copy-code]
+#   bash setup-docsify.sh
 #
-# Options:
-#   --with-prism       Also download Prism and enable syntax highlighting in index.html
-#   --with-copy-code   Also download the docsify-copy-code plugin (copy button on code blocks)
+# Downloads Docsify core, the search plugin, the Vue theme, the copy-to-clipboard
+# plugin, and Prism syntax highlighting (bash, yaml, javascript, python, r) — all
+# served locally, no external CDN dependencies at runtime.
+#
+# Re-running in an existing site is safe: it refreshes the assets and regenerates
+# index.html, but never overwrites Markdown files (README.md, _sidebar.md, and any
+# pages you have added) that already exist.
 
 set -euo pipefail
 
 # ── Configuration ───────────────────────────────────────────────────────────────
 # Use "4" for the latest 4.x release, or pin to a specific version e.g. "4.13.1"
 DOCSIFY_VERSION="4"
-PRISM=false
-COPY_CODE=false
 
-# ── Argument parsing ────────────────────────────────────────────────────────────
-for arg in "$@"; do
-  case "$arg" in
-    --with-prism) PRISM=true ;;
-    --with-copy-code) COPY_CODE=true ;;
-    *) echo "Unknown option: $arg" >&2; exit 1 ;;
-  esac
-done
+# ── Argument check ──────────────────────────────────────────────────────────────
+if [[ $# -gt 0 ]]; then
+  echo "This script takes no options (got: $*)." >&2
+  echo "Usage: bash setup-docsify.sh" >&2
+  exit 1
+fi
 
 # ── Output helpers ──────────────────────────────────────────────────────────────
 GREEN='\033[0;32m'
 BLUE='\033[0;34m'
+YELLOW='\033[0;33m'
 RED='\033[0;31m'
 BOLD='\033[1m'
 NC='\033[0m'
 
 step() { echo -e "\n${BLUE}${BOLD}==> $1${NC}"; }
 ok()   { echo -e "  ${GREEN}✓${NC}  $1"; }
+skip() { echo -e "  ${YELLOW}•${NC}  $1"; }
 die()  { echo -e "  ${RED}✗${NC}  $1" >&2; exit 1; }
 
 # ── Preflight checks ────────────────────────────────────────────────────────────
@@ -46,7 +48,8 @@ ok "curl $(curl --version | head -1 | awk '{print $2}')"
 
 if [[ -f index.html ]]; then
   echo -e "  ${RED}!${NC}  index.html already exists in: $(pwd)"
-  echo -e "       This script will overwrite index.html and all boilerplate .md files."
+  echo -e "       This re-downloads assets and regenerates index.html (edits to"
+  echo -e "       index.html will be lost). Existing Markdown files are left untouched."
   read -r -p "       Continue? [y/N] " reply
   [[ "${reply,,}" == "y" ]] || { echo "Aborted."; exit 0; }
 fi
@@ -71,33 +74,30 @@ fetch() {
   ok "$dest"
 }
 
-fetch "${CDN}/docsify@${DOCSIFY_VERSION}/lib/docsify.min.js"        assets/js/docsify.min.js
-fetch "${CDN}/docsify@${DOCSIFY_VERSION}/lib/plugins/search.min.js" assets/js/search.min.js
+# Core Docsify, search plugin, and theme
+fetch "${CDN}/docsify@${DOCSIFY_VERSION}/lib/docsify.min.js"         assets/js/docsify.min.js
+fetch "${CDN}/docsify@${DOCSIFY_VERSION}/lib/plugins/search.min.js"  assets/js/search.min.js
 fetch "${CDN}/docsify@${DOCSIFY_VERSION}/themes/vue.css"             assets/css/vue.css
 
-if [[ "$PRISM" == true ]]; then
-  echo ""
-  echo "  Downloading Prism syntax highlighting..."
-  fetch "${CDN}/prismjs@1/components/prism-core.min.js"        assets/js/prism-core.min.js
-  fetch "${CDN}/prismjs@1/components/prism-bash.min.js"        assets/js/prism-bash.min.js
-  fetch "${CDN}/prismjs@1/components/prism-yaml.min.js"        assets/js/prism-yaml.min.js
-  fetch "${CDN}/prismjs@1/components/prism-javascript.min.js"  assets/js/prism-javascript.min.js
-fi
+# Copy-to-clipboard plugin (injects its own CSS — no separate stylesheet needed)
+fetch "${CDN}/docsify-copy-code@3/dist/docsify-copy-code.min.js"    assets/js/docsify-copy-code.min.js
 
-if [[ "$COPY_CODE" == true ]]; then
-  echo ""
-  echo "  Downloading copy-to-clipboard plugin..."
-  fetch "${CDN}/docsify-copy-code@3/dist/docsify-copy-code.min.js"  assets/js/docsify-copy-code.min.js
-fi
+# Prism syntax highlighting: core engine, then clike (required by javascript),
+# then the individual languages.
+fetch "${CDN}/prismjs@1/components/prism-core.min.js"        assets/js/prism-core.min.js
+fetch "${CDN}/prismjs@1/components/prism-clike.min.js"       assets/js/prism-clike.min.js
+fetch "${CDN}/prismjs@1/components/prism-javascript.min.js"  assets/js/prism-javascript.min.js
+fetch "${CDN}/prismjs@1/components/prism-bash.min.js"        assets/js/prism-bash.min.js
+fetch "${CDN}/prismjs@1/components/prism-yaml.min.js"        assets/js/prism-yaml.min.js
+fetch "${CDN}/prismjs@1/components/prism-python.min.js"      assets/js/prism-python.min.js
+fetch "${CDN}/prismjs@1/components/prism-r.min.js"           assets/js/prism-r.min.js
 
 # ── Step 3: index.html ──────────────────────────────────────────────────────────
 step "Step 3 — Creating index.html"
 
-# index.html is assembled in parts so the Prism <script> block can be
-# included or omitted cleanly. The heredoc delimiters are single-quoted
-# ('HTML_HEAD') to prevent the shell from expanding $docsify.
-{
-  cat << 'HTML_HEAD'
+# The heredoc delimiter is single-quoted ('HTML') so the shell does not expand
+# $docsify inside the template.
+cat > index.html << 'HTML'
 <!DOCTYPE html>
 <html lang="en">
 <head>
@@ -119,39 +119,40 @@ step "Step 3 — Creating index.html"
   </script>
   <script src="assets/js/docsify.min.js"></script>
   <script src="assets/js/search.min.js"></script>
-HTML_HEAD
-
-  if [[ "$COPY_CODE" == true ]]; then
-    cat << 'HTML_COPYCODE'
-
-  <!-- Copy-to-clipboard button for code blocks -->
   <script src="assets/js/docsify-copy-code.min.js"></script>
-HTML_COPYCODE
-  fi
-
-  if [[ "$PRISM" == true ]]; then
-    cat << 'HTML_PRISM'
 
-  <!-- Prism syntax highlighting -->
+  <!-- Prism: core engine first, then clike (required by javascript), then languages -->
   <script src="assets/js/prism-core.min.js"></script>
+  <script src="assets/js/prism-clike.min.js"></script>
+  <script src="assets/js/prism-javascript.min.js"></script>
   <script src="assets/js/prism-bash.min.js"></script>
   <script src="assets/js/prism-yaml.min.js"></script>
-  <script src="assets/js/prism-javascript.min.js"></script>
-HTML_PRISM
-  fi
-
-  cat << 'HTML_FOOT'
+  <script src="assets/js/prism-python.min.js"></script>
+  <script src="assets/js/prism-r.min.js"></script>
 </body>
 </html>
-HTML_FOOT
-} > index.html
+HTML
 
 ok "index.html"
 
 # ── Step 4: Boilerplate content ─────────────────────────────────────────────────
-step "Step 4 — Creating boilerplate content"
+step "Step 4 — Boilerplate content (created only if missing)"
+
+# Write the heredoc on stdin to $1, but never clobber an existing file — so
+# re-running refreshes the assets and index.html without touching your content.
+write_boilerplate() {
+  local dest="$1"
+  local content
+  content="$(cat)"
+  if [[ -e "$dest" ]]; then
+    skip "$dest (exists — left unchanged)"
+  else
+    printf '%s\n' "$content" > "$dest"
+    ok "$dest"
+  fi
+}
 
-cat > README.md << 'EOF'
+write_boilerplate README.md << 'EOF'
 # Welcome
 
 This is the home page of your documentation site.
@@ -161,15 +162,13 @@ Edit `README.md` to replace this content.
 
 - [Getting Started](getting-started.md)
 EOF
-ok "README.md"
 
-cat > _sidebar.md << 'EOF'
+write_boilerplate _sidebar.md << 'EOF'
 - [Home](/)
 - [Getting Started](getting-started.md)
 EOF
-ok "_sidebar.md"
 
-cat > getting-started.md << 'EOF'
+write_boilerplate getting-started.md << 'EOF'
 # Getting Started
 
 This is an example page. Replace this content with your own documentation.
@@ -183,7 +182,6 @@ Write your content here using standard Markdown.
 Docsify will automatically generate sidebar anchors for H2 headings
 when `subMaxLevel: 2` is set in `index.html`.
 EOF
-ok "getting-started.md"
 
 # ── Step 5: Permissions ─────────────────────────────────────────────────────────
 step "Step 5 — Setting file permissions"
@@ -201,15 +199,8 @@ find . -not -path '*/\.*' | sort
 echo ""
 echo -e "${GREEN}${BOLD}Setup complete.${NC}"
 echo -e "Open your site in a browser to verify."
-
-if [[ "$PRISM" == true ]]; then
-  echo ""
-  echo -e "Prism is enabled for: bash, yaml, javascript."
-  echo -e "To add more languages, download additional prism-*.min.js files"
-  echo -e "into assets/js/ and add their <script> tags to index.html."
-fi
-
-if [[ "$COPY_CODE" == true ]]; then
-  echo ""
-  echo -e "Copy-to-clipboard buttons are enabled on all code blocks."
-fi
+echo ""
+echo -e "Syntax highlighting (Prism) is enabled for: bash, yaml, javascript, python, r."
+echo -e "To add more languages, download additional prism-*.min.js files into"
+echo -e "assets/js/ and add their <script> tags to index.html (after prism-core.min.js)."
+echo -e "Copy-to-clipboard buttons are enabled on all code blocks."