Clean up infrastructure: remove dead code, fix watch script, fix typos

- Remove hugo.sh (broken draft superseded by hugo-new.sh)
- Remove unused mermaid shortcode and partial (only code-block
  rendering via render-codeblock-mermaid.html is used)
- Remove dead xparams.mermaid check from extend_head.html
- Fix watch-rmd.sh to pass shared libs args matching the Makefile
- Fix typos in Makefile ("permsions", "Publising")

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Makefile

@@ -42,7 +42,7 @@ publish: build #> Publish site
 	@#   safe-links: ignore symlinks that point outside of tree
 	@#   times:      preserve modification times
 	@#   delete:     delete extraneous files, i.e., files on destination
-	@#   chmod:      set permsions
+	@#   chmod:      set permissions
 	@echo "\t 📡 Copying from public to ${DEST}"
 	@rsync \
 	  --verbose \
@@ -56,7 +56,7 @@ publish: build #> Publish site
 	  ${DEST}
 	@echo "\t 🛡️ Setting permissions"
 	@ssh axs@sdf.org 'mkhomepg -p'
-	@echo "✓ Publising complete"
+	@echo "✓ Publishing complete"
 	@echo "\nThe site should be available on ${SITE_URL}"
 
 serve: #> Start a Hugo server

hugo.sh

@@ -1,47 +0,0 @@
-#!/bin/bash
-set -e
-
-# Usage: ./hugo-new.sh "<title>" [md|rmd]
-
-TITLE="$2"
-EXTENSION="${1:-rmd}"  # default to Rmd if not specified
-
-# Validate extension
-if [[ "$EXTENSION" != "md" && "$EXTENSION" != "rmd" ]]; then
-    echo "⚠️  Usage: ./hugo-new.sh \"Post Title\" [md|rmd]"
-    exit 1
-fi
-
-DATE=$(date '+%Y-%m-%d')
-SLUG=$(echo "$TITLE" | tr '[:upper:]' '[:lower:]' | tr ' ' '-')
-POST_DIR="content/posts/${DATE}-${SLUG}"
-
-# Create new post using Hugo archetype
-if [ "$EXTENSION" == "rmd" ]; then
-    POST_FILE="index.Rmd"
-else
-    POST_DIR="content/posts/${DATE}-${SLUG}"
-    EXTENSION="md"
-fi
-
-hugo new "posts/${DATE}-${SLUG}/index.${EXTENSION}"
-
-# Change to post directory
-cd "$POST_DIR"
-
-# Set up .gitignore and renv (for R Markdown)
-if [ "$EXTENSION" == "rmd" ]; then
-    # Ignore generated Markdown file
-    echo "index.md" > .gitignore
-
-    # Set up minimal renv environment from base snapshot
-    cp ../../../../scripts/base-renv.lock ./renv.lock
-
-    Rscript -e '
-      if (!require("renv")) install.packages("renv");
-      renv::init(bare = TRUE);
-      renv::restore();
-    '
-fi
-
-echo "✅ Created post at ${POST_DIR}/index.${EXTENSION}"

layouts/partials/extend_head.html

@@ -3,10 +3,5 @@
   {{ partialCached "math.html" . }}
 {{ end }}
 
-<!-- Mermaid diagrams -->
-{{ if .Params.xparams.mermaid }}
-  {{ partialCached "mermaid.html" . }}
-{{ end }}
-
 <!-- React components -->
 {{- partial "react.html" . -}}

layouts/partials/mermaid.html

@@ -1,5 +0,0 @@
-<!-- Mermaid JS -->
-<script src="https://cdn.jsdelivr.net/npm/mermaid@11.4.1/dist/mermaid.min.js"></script>
-<script>
-  mermaid.initialize({ startOnLoad: true });
-</script>

layouts/shortcodes/mermaid.html

@@ -1,6 +0,0 @@
-{{ $align := .Get "align" | default "center" }}
-<div style="text-align: {{ $align }};">
-  <div class="mermaid">
-    {{ .Inner | safeHTML }}
-  </div>
-</div>

scripts/watch-rmd.sh

@@ -1,5 +1,8 @@
 #!/bin/bash
 WATCH_DIR="content/posts"
+PROJECT_ROOT="$(cd "$(dirname "$0")/.." && pwd)"
+LIBS_DIR="static/libs"
+LIBS_URL="/libs"
 
 echo "🚨 Watching ${WATCH_DIR} for changes..."
 
@@ -9,7 +12,7 @@ inotifywait -m -e close_write --format '%w%f' -r "$WATCH_DIR" | while read FILE;
 
         echo "🔄 Change detected in $FILE. Rendering..."
 
-        (cd "$POST_DIR" && Rscript -e 'renv::restore(prompt = FALSE); statdown::statdown_render("index.Rmd")')
+        (cd "$POST_DIR" && Rscript -e 'renv::restore(prompt = FALSE); statdown::statdown_render("index.Rmd", output_root = "'"${PROJECT_ROOT}/${LIBS_DIR}"'", url_root = "'"${LIBS_URL}"'")')
 
         echo "✅ Rendered ${FILE}"
     fi