From fdb49ba5d1f72f972449d408ac81f2599af7a17f Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 12 Nov 2026 21:26:58 +0000
Subject: [PATCH 1/2] Save the theme under lds-theme, reading mln-theme as a
 fallback

mcs, pds, sds, psw and lds already store the reader's palette under
lds-theme. qwt still used mln-theme, so the weekly site-scaffolding sync
would open PRs downstream that switch them back, and readers would lose
the theme they chose. The two files are now byte-identical to pds's
copies, which also match lds and sds for theme-picker.html.

Closes #215

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_019xfc9qigfPPFGGNdUMwT33
---
 CLAUDE.md              |  2 +-
 qwt-reveal-toggle.html | 12 +++++++-----
 theme-picker.html      |  9 +++++----
 3 files changed, 13 insertions(+), 10 deletions(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index f6b1a3b1..3f36f902 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -22,7 +22,7 @@ Authoritative style guides:
 - `latex-macros/` --- git submodule for shortcode/macro definitions (see `.gitmodules`)
 - `R/`, `man/`, `DESCRIPTION`, `NAMESPACE` --- the project is also a small R package
 - `references.bib` --- BibTeX bibliography
-- `offwhite.scss`, `theme-picker.html` --- the website's Light / Off-white / Parchment / Dark theme dropdown (`theme-picker.html` builds it, `offwhite.scss` styles the two tinted palettes); the choice is saved under `mln-theme`, shared with the slides and with the other sites on this origin
+- `offwhite.scss`, `theme-picker.html` --- the website's Light / Off-white / Parchment / Dark theme dropdown (`theme-picker.html` builds it, `offwhite.scss` styles the two tinted palettes); the choice is saved under `lds-theme` (reading the older `mln-theme` as a fallback), shared with the slides and with the other sites on this origin
 - `page-navigation.html` --- HTML include (`format.html.include-after-body`) that adds floating previous/next arrows in the page margins and fixes navbar highlighting now that Home is in the sidebar; vendored from `Morrison-Lab/lbt` (a private repo, so not linked)
 - `anchor-landing.html` --- HTML include (`format.html.include-after-body`) that keeps the reader's place while equations and images change the page height
   (the same file as in `Morrison-Lab/lds`)
diff --git a/qwt-reveal-toggle.html b/qwt-reveal-toggle.html
index fbbbf913..0f0e8bdf 100644
--- a/qwt-reveal-toggle.html
+++ b/qwt-reveal-toggle.html
@@ -6,9 +6,10 @@
   reads those vars so it stays legible in every palette. Light is the
   default variable set, Off-white and Parchment are a data-palette attribute
   on <html>, and Dark is the body.qwt-dark class. The choice is saved under
-  "mln-theme", the key the website's theme dropdown (theme-picker.html) uses,
-  so it carries across the site and the decks. First-time visitors get
-  Dark if their system prefers it, and Off-white otherwise.
+  "lds-theme" (falling back to "mln-theme"), the key the website's theme
+  dropdown (theme-picker.html) uses, so it carries across the site and the
+  decks. First-time visitors get Dark if their system prefers it, and
+  Off-white otherwise.
 -->
 <style>
   #qwt-theme-select {
@@ -42,7 +43,8 @@
 <script>
 (function () {
   "use strict";
-  var KEY = "mln-theme";
+  var KEY = "lds-theme";
+  var LEGACY_KEY = "mln-theme";
   var DARK_CLASS = "qwt-dark";
   var OPTIONS = [["light", "Light"], ["offwhite", "Off-white"], ["parchment", "Parchment"], ["dark", "Dark"]];
   var root = document.documentElement;
@@ -52,7 +54,7 @@
   }
 
   function stored() {
-    try { return localStorage.getItem(KEY); } catch (e) { return null; }
+    try { return localStorage.getItem(KEY) || localStorage.getItem(LEGACY_KEY); } catch (e) { return null; }
   }
 
   function initialTheme() {
diff --git a/theme-picker.html b/theme-picker.html
index 21ad3ded..6051aca9 100644
--- a/theme-picker.html
+++ b/theme-picker.html
@@ -1,13 +1,14 @@
 <script>
 // Theme dropdown: Light, Off-white, Parchment, Dark. Quarto's own toggle
 // handles light/dark and remembers it; the two tinted palettes are a
-// data-palette attribute on <html>. The choice is kept under "mln-theme".
-// Off-white is the default for a first visit.
+// data-palette attribute on <html>. The choice is kept under "lds-theme"
+// (falling back to "mln-theme"). Off-white is the default for a first visit.
 (function () {
-  var KEY = "mln-theme";
+  var KEY = "lds-theme";
+  var LEGACY_KEY = "mln-theme";
   var OPTIONS = [["light", "Light"], ["offwhite", "Off-white"], ["parchment", "Parchment"], ["dark", "Dark"]];
   function stored() {
-    try { return localStorage.getItem(KEY); } catch (e) { return null; }
+    try { return localStorage.getItem(KEY) || localStorage.getItem(LEGACY_KEY); } catch (e) { return null; }
   }
   function isDark() { return document.body.classList.contains("quarto-dark"); }
   function apply(choice, remember) {

From 1916f9a8cd4a85e0513f17570ff57dc45fdd757b Mon Sep 17 00:00:00 2001
From: Claude <noreply@anthropic.com>
Date: Thu, 12 Nov 2026 21:28:15 +0000
Subject: [PATCH 2/2] Break the CLAUDE.md theme bullet at its semicolon

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Claude-Session: https://claude.ai/code/session_019xfc9qigfPPFGGNdUMwT33
---
 CLAUDE.md | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/CLAUDE.md b/CLAUDE.md
index 3f36f902..8e42ee33 100644
--- a/CLAUDE.md
+++ b/CLAUDE.md
@@ -22,7 +22,8 @@ Authoritative style guides:
 - `latex-macros/` --- git submodule for shortcode/macro definitions (see `.gitmodules`)
 - `R/`, `man/`, `DESCRIPTION`, `NAMESPACE` --- the project is also a small R package
 - `references.bib` --- BibTeX bibliography
-- `offwhite.scss`, `theme-picker.html` --- the website's Light / Off-white / Parchment / Dark theme dropdown (`theme-picker.html` builds it, `offwhite.scss` styles the two tinted palettes); the choice is saved under `lds-theme` (reading the older `mln-theme` as a fallback), shared with the slides and with the other sites on this origin
+- `offwhite.scss`, `theme-picker.html` --- the website's Light / Off-white / Parchment / Dark theme dropdown (`theme-picker.html` builds it, `offwhite.scss` styles the two tinted palettes);
+  the choice is saved under `lds-theme` (reading the older `mln-theme` as a fallback), shared with the slides and with the other sites on this origin
 - `page-navigation.html` --- HTML include (`format.html.include-after-body`) that adds floating previous/next arrows in the page margins and fixes navbar highlighting now that Home is in the sidebar; vendored from `Morrison-Lab/lbt` (a private repo, so not linked)
 - `anchor-landing.html` --- HTML include (`format.html.include-after-body`) that keeps the reader's place while equations and images change the page height
   (the same file as in `Morrison-Lab/lds`)