From f4b1523ed4ba5ae7a70e1a31b6f0b3b7e678f116 Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sat, 7 Feb 2026 13:51:43 +0000
Subject: [PATCH 01/10] Add CI check for thesis nav docs sync

---
 .github/workflows/jekyll.yml         |  5 ++++
 scripts/check-phd-thesis-nav-docs.sh | 45 ++++++++++++++++++++++++++++
 2 files changed, 50 insertions(+)
 create mode 100755 scripts/check-phd-thesis-nav-docs.sh

diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
index 0efb4248..549e1733 100644
--- a/.github/workflows/jekyll.yml
+++ b/.github/workflows/jekyll.yml
@@ -16,6 +16,11 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
+
+    - name: Verify thesis navigation docs stay in sync
+      run: |
+        chmod +x scripts/check-phd-thesis-nav-docs.sh
+        ./scripts/check-phd-thesis-nav-docs.sh
     
     - name: Set up Ruby
       uses: ruby/setup-ruby@v1
diff --git a/scripts/check-phd-thesis-nav-docs.sh b/scripts/check-phd-thesis-nav-docs.sh
new file mode 100755
index 00000000..5d1b592d
--- /dev/null
+++ b/scripts/check-phd-thesis-nav-docs.sh
@@ -0,0 +1,45 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+REPO_ROOT="$(cd "$(dirname "${BASH_SOURCE[0]}")/.." && pwd)"
+LAYOUT_FILE="${REPO_ROOT}/_layouts/default.html"
+DOC_FILE="${REPO_ROOT}/AGENTS.md"
+
+NAV_LINK='href="{{ site.baseurl }}/phd-thesis/"'
+DOC_PHRASE="This page is included in the main navigation menu"
+
+if [[ ! -f "${LAYOUT_FILE}" ]]; then
+  echo "Missing layout file: ${LAYOUT_FILE}"
+  exit 1
+fi
+
+if [[ ! -f "${DOC_FILE}" ]]; then
+  echo "Missing docs file: ${DOC_FILE}"
+  exit 1
+fi
+
+nav_present=0
+doc_phrase_present=0
+
+if grep -Fq "${NAV_LINK}" "${LAYOUT_FILE}"; then
+  nav_present=1
+fi
+
+if grep -Fq "${DOC_PHRASE}" "${DOC_FILE}"; then
+  doc_phrase_present=1
+fi
+
+if [[ ${nav_present} -eq 1 && ${doc_phrase_present} -eq 0 ]]; then
+  echo "PhD thesis nav link exists but docs are stale."
+  echo "Update AGENTS.md to mention thesis page is in main navigation."
+  exit 1
+fi
+
+if [[ ${nav_present} -eq 0 && ${doc_phrase_present} -eq 1 ]]; then
+  echo "Docs mention thesis page in main navigation but nav link is missing."
+  echo "Update AGENTS.md or restore nav link in _layouts/default.html."
+  exit 1
+fi
+
+echo "PhD thesis nav/docs check passed."

From e476fa129566eb576c1714dcae1581086c31aadd Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sat, 7 Feb 2026 13:52:16 +0000
Subject: [PATCH 02/10] Pin MathJax and document inline delimiter policy

---
 AGENTS.md             | 9 +++++++++
 _layouts/default.html | 3 ++-
 2 files changed, 11 insertions(+), 1 deletion(-)

diff --git a/AGENTS.md b/AGENTS.md
index a61d57e3..f44451e6 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -82,6 +82,15 @@ The following pages redirect to the CoMPhy Lab website:
 - **\_layouts/default.html**: Base template for all pages
 - **Gemfile**: Ruby dependencies including Jekyll 4.3.2 and various
   plugins
+- **MathJax**: Loaded from pinned CDN version
+  (`https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-svg.js`) to keep
+  rendering reproducible.
+
+### Math Authoring Policy
+
+- Inline math supports both `\(...\)` and `$...$`.
+- Escape literal dollar signs in content as `\$` to prevent accidental math
+  parsing.
 
 ### Content Management
 
diff --git a/_layouts/default.html b/_layouts/default.html
index 49959315..7ce72f69 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -28,6 +28,7 @@
   <script>
     window.MathJax = {
       tex: {
+        // Keep $...$ support for existing content; escape literal currency as \$.
         inlineMath: [['\\(', '\\)'], ['$', '$']]
       },
       svg: {
@@ -35,7 +36,7 @@
       }
     };
   </script>
-  <script defer src="{{ site.baseurl }}/assets/js/mathjax/tex-svg.js"></script>
+  <script defer src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-svg.js"></script>
 
   <script>
     document.documentElement.classList.remove('no-js');

From fa12f9cccdd405120c62cd7409042f12018023d2 Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sat, 7 Feb 2026 13:53:37 +0000
Subject: [PATCH 03/10] Enforce MD034 and normalize markdown bare URLs

---
 .markdownlint-cli2.jsonc | 10 ++++++++++
 README.md                |  2 +-
 2 files changed, 11 insertions(+), 1 deletion(-)
 create mode 100644 .markdownlint-cli2.jsonc

diff --git a/.markdownlint-cli2.jsonc b/.markdownlint-cli2.jsonc
new file mode 100644
index 00000000..57aab723
--- /dev/null
+++ b/.markdownlint-cli2.jsonc
@@ -0,0 +1,10 @@
+{
+  "config": {
+    "default": false,
+    "MD034": true
+  },
+  "ignores": [
+    "node_modules/**",
+    "assets/css/academicons-1.7.0/README.md"
+  ]
+}
diff --git a/README.md b/README.md
index c9eaf513..5633868c 100644
--- a/README.md
+++ b/README.md
@@ -55,7 +55,7 @@ The personal website for Vatsal Sanjay, hosted at [comphy-lab.org/vatsalsy](http
    ```bash
    bundle exec jekyll serve
    ```
-   - Visit http://localhost:4000 in the browser
+   - Visit <http://localhost:4000> in the browser
    - Changes in source files trigger automatic rebuilds
 
 4. **Deployment**

From f5f2e4b43b309946dc828fe48919d1a096aee0eb Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sat, 7 Feb 2026 13:54:07 +0000
Subject: [PATCH 04/10] Add diagnostics for missing search database updates

---
 .github/workflows/update-search.yml | 19 +++++++++++++++++++
 1 file changed, 19 insertions(+)

diff --git a/.github/workflows/update-search.yml b/.github/workflows/update-search.yml
index 89914408..b905053d 100644
--- a/.github/workflows/update-search.yml
+++ b/.github/workflows/update-search.yml
@@ -46,16 +46,28 @@ jobs:
           else
             echo "Warning: Could not clone ${GITHUB_ORG}/${SEARCH_REPO}"
             echo "Search functionality may be limited. This is expected if the search repository does not exist."
+            echo "::warning title=Search DB clone failed::Could not clone ${GITHUB_ORG}/${SEARCH_REPO}. Search update will be skipped."
+            {
+              echo "### Search DB update skipped"
+              echo "- Clone failed for \`${GITHUB_ORG}/${SEARCH_REPO}\`."
+            } >> "${GITHUB_STEP_SUMMARY}"
             exit 0
           fi
 
       - name: Copy search database
+        id: copy-search-db
         run: |
           SEARCH_REPO="${SEARCH_REPO:-comphy-search}"
+          echo "search_db_available=false" >> "${GITHUB_OUTPUT}"
 
           if [ ! -d "${SEARCH_REPO}" ]; then
             echo "Warning: ${SEARCH_REPO} directory not found (clone may have failed)"
             echo "Search functionality will be limited"
+            echo "::warning title=Search DB directory missing::Directory ${SEARCH_REPO} was not found."
+            {
+              echo "### Search DB update skipped"
+              echo "- Directory \`${SEARCH_REPO}\` was not found after clone."
+            } >> "${GITHUB_STEP_SUMMARY}"
             exit 0
           fi
 
@@ -63,14 +75,21 @@ jobs:
 
           if [ -f "${SEARCH_REPO}/search_db.json" ]; then
             cp "${SEARCH_REPO}/search_db.json" assets/js/search_db.json
+            echo "search_db_available=true" >> "${GITHUB_OUTPUT}"
             echo "Search database copied successfully"
           else
             echo "Warning: search_db.json not found in ${SEARCH_REPO}"
             echo "Search functionality will be limited"
+            echo "::warning title=search_db.json missing::No search_db.json found in ${SEARCH_REPO}."
+            {
+              echo "### Search DB update skipped"
+              echo "- Missing \`${SEARCH_REPO}/search_db.json\`."
+            } >> "${GITHUB_STEP_SUMMARY}"
             exit 0
           fi
 
       - name: Commit and push changes
+        if: steps.copy-search-db.outputs.search_db_available == 'true'
         run: |
           git config --local user.name 'comphy-search-updater[bot]'
           git config --local user.email "${{ env.APP_BOT_USER_ID }}+comphy-search-updater[bot]@users.noreply.github.com"

From 806e95a2b9f18f662adbe18a33e983f6a9c9e2b2 Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sat, 7 Feb 2026 13:54:38 +0000
Subject: [PATCH 05/10] Block node_modules diffs in CI workflows

---
 .github/workflows/jekyll.yml | 35 +++++++++++++++++++++++++++++++++++
 1 file changed, 35 insertions(+)

diff --git a/.github/workflows/jekyll.yml b/.github/workflows/jekyll.yml
index 549e1733..13b293eb 100644
--- a/.github/workflows/jekyll.yml
+++ b/.github/workflows/jekyll.yml
@@ -16,6 +16,41 @@ jobs:
     runs-on: ubuntu-latest
     steps:
     - uses: actions/checkout@v4
+      with:
+        fetch-depth: 0
+
+    - name: Block node_modules changes on pull requests
+      if: github.event_name == 'pull_request'
+      run: |
+        BASE_SHA="${{ github.event.pull_request.base.sha }}"
+        HEAD_SHA="${{ github.event.pull_request.head.sha }}"
+        CHANGED_NODE_MODULES="$(git diff --name-only "${BASE_SHA}...${HEAD_SHA}" -- 'node_modules/**')"
+
+        if [ -n "${CHANGED_NODE_MODULES}" ]; then
+          echo "::error title=Blocked path::Pull request includes changes under node_modules/."
+          echo "${CHANGED_NODE_MODULES}"
+          exit 1
+        fi
+
+    - name: Block node_modules changes on pushes
+      if: github.event_name == 'push'
+      run: |
+        BASE_SHA="${{ github.event.before }}"
+        HEAD_SHA="${{ github.sha }}"
+        ZERO_SHA="0000000000000000000000000000000000000000"
+
+        if [ "${BASE_SHA}" = "${ZERO_SHA}" ]; then
+          echo "Initial push detected; skipping node_modules diff guard."
+          exit 0
+        fi
+
+        CHANGED_NODE_MODULES="$(git diff --name-only "${BASE_SHA}...${HEAD_SHA}" -- 'node_modules/**')"
+
+        if [ -n "${CHANGED_NODE_MODULES}" ]; then
+          echo "::error title=Blocked path::Push includes changes under node_modules/."
+          echo "${CHANGED_NODE_MODULES}"
+          exit 1
+        fi
 
     - name: Verify thesis navigation docs stay in sync
       run: |

From 5e98e677489418f5d14518b0c191ad87aae1e373 Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sun, 8 Feb 2026 13:19:27 +0000
Subject: [PATCH 06/10] Prefer local MathJax with CDN fallback

Load the vendored tex-svg.js asset first for reliability and offline support.

If local loading fails, fall back to pinned jsDelivr with SRI and crossorigin.

Update AGENTS.md to document the local-primary, CDN-fallback policy.
---
 AGENTS.md             | 7 ++++---
 _layouts/default.html | 6 +++++-
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/AGENTS.md b/AGENTS.md
index f44451e6..d47417c0 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -82,9 +82,10 @@ The following pages redirect to the CoMPhy Lab website:
 - **\_layouts/default.html**: Base template for all pages
 - **Gemfile**: Ruby dependencies including Jekyll 4.3.2 and various
   plugins
-- **MathJax**: Loaded from pinned CDN version
-  (`https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-svg.js`) to keep
-  rendering reproducible.
+- **MathJax**: Loaded from local vendored asset first
+  (`/assets/js/mathjax/tex-svg.js`) with a pinned jsDelivr fallback
+  (`https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-svg.js`, with SRI)
+  for runtime resilience.
 
 ### Math Authoring Policy
 
diff --git a/_layouts/default.html b/_layouts/default.html
index 7ce72f69..d8f995d7 100644
--- a/_layouts/default.html
+++ b/_layouts/default.html
@@ -36,7 +36,11 @@
       }
     };
   </script>
-  <script defer src="https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-svg.js"></script>
+  <script
+    defer
+    src="{{ site.baseurl }}/assets/js/mathjax/tex-svg.js"
+    onerror="this.onerror=null;this.crossOrigin='anonymous';this.integrity='sha384-KKWa9jJ1MZvssLeOoXG6FiOAZfAgmzsIIfw8BXwI9+kYm0lPCbC6yTQPBC00F1/L';this.src='https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-svg.js';"
+  ></script>
 
   <script>
     document.documentElement.classList.remove('no-js');

From 13e9eff6c1050d69018c9ffeabf7b4dcb3329fcb Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sun, 8 Feb 2026 13:33:54 +0000
Subject: [PATCH 07/10] Restore markdownlint default rule coverage

---
 .markdownlint-cli2.jsonc | 8 ++------
 1 file changed, 2 insertions(+), 6 deletions(-)

diff --git a/.markdownlint-cli2.jsonc b/.markdownlint-cli2.jsonc
index 57aab723..45757da9 100644
--- a/.markdownlint-cli2.jsonc
+++ b/.markdownlint-cli2.jsonc
@@ -1,10 +1,6 @@
 {
   "config": {
-    "default": false,
-    "MD034": true
+    "MD034": true,
   },
-  "ignores": [
-    "node_modules/**",
-    "assets/css/academicons-1.7.0/README.md"
-  ]
+  "ignores": ["node_modules/**", "assets/css/academicons-1.7.0/README.md"],
 }

From 69774bf19f1e8ca512a5243c353a302cc60bf835 Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sun, 8 Feb 2026 13:33:59 +0000
Subject: [PATCH 08/10] Gate search DB copy on clone success

---
 .github/workflows/update-search.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/update-search.yml b/.github/workflows/update-search.yml
index b905053d..e7949b50 100644
--- a/.github/workflows/update-search.yml
+++ b/.github/workflows/update-search.yml
@@ -35,6 +35,7 @@ jobs:
           fetch-depth: 0 # Fetch all history for proper git operations
 
       - name: Clone comphy-search repository
+        id: clone-search-repo
         run: |
           GITHUB_ORG="${GITHUB_REPOSITORY%%/*}"
           SEARCH_REPO="${SEARCH_REPO:-comphy-search}"
@@ -42,8 +43,10 @@ jobs:
 
           if git clone "https://github.com/${GITHUB_ORG}/${SEARCH_REPO}.git"; then
             mkdir -p assets/js
+            echo "clone_ok=true" >> "${GITHUB_OUTPUT}"
             echo "Search database repository cloned successfully"
           else
+            echo "clone_ok=false" >> "${GITHUB_OUTPUT}"
             echo "Warning: Could not clone ${GITHUB_ORG}/${SEARCH_REPO}"
             echo "Search functionality may be limited. This is expected if the search repository does not exist."
             echo "::warning title=Search DB clone failed::Could not clone ${GITHUB_ORG}/${SEARCH_REPO}. Search update will be skipped."
@@ -56,6 +59,7 @@ jobs:
 
       - name: Copy search database
         id: copy-search-db
+        if: steps.clone-search-repo.outputs.clone_ok == 'true'
         run: |
           SEARCH_REPO="${SEARCH_REPO:-comphy-search}"
           echo "search_db_available=false" >> "${GITHUB_OUTPUT}"

From 95fbcf7fcb91f945a2c0df551af1dc5594dcee64 Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sun, 8 Feb 2026 13:34:04 +0000
Subject: [PATCH 09/10] Clarify MathJax reproducibility tradeoff

---
 AGENTS.md | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/AGENTS.md b/AGENTS.md
index d47417c0..146e1a07 100644
--- a/AGENTS.md
+++ b/AGENTS.md
@@ -82,10 +82,11 @@ The following pages redirect to the CoMPhy Lab website:
 - **\_layouts/default.html**: Base template for all pages
 - **Gemfile**: Ruby dependencies including Jekyll 4.3.2 and various
   plugins
-- **MathJax**: Loaded from local vendored asset first
-  (`/assets/js/mathjax/tex-svg.js`) with a pinned jsDelivr fallback
+- **MathJax**: Loaded from the local vendored asset first
+  (`/assets/js/mathjax/tex-svg.js`) for offline and archival reproducibility,
+  with a pinned jsDelivr fallback
   (`https://cdn.jsdelivr.net/npm/mathjax@3.2.2/es5/tex-svg.js`, with SRI)
-  for runtime resilience.
+  for consistent behavior when online (requires CDN availability).
 
 ### Math Authoring Policy
 

From 4650f011f0e9f537cc89a2593b9d2658cf08e1d0 Mon Sep 17 00:00:00 2001
From: Vatsal Sanjay <vatsal.sanjay@comphy-lab.org>
Date: Sun, 8 Feb 2026 13:34:16 +0000
Subject: [PATCH 10/10] update gitignore

---
 .gitignore | 1 +
 1 file changed, 1 insertion(+)

diff --git a/.gitignore b/.gitignore
index 69eb34f3..b1246c4c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,3 +1,4 @@
+.comphy
 _site/
 .sass-cache/
 .jekyll-cache/