refactor(extensions): rename mlsysbook to mlsysbook-ext for clearer naming

- Rename mlsysbook/ → mlsysbook-ext/ for explicit extension identification
- Update all Quarto configuration files to use new paths
- Update Lua filter references to new configuration keys
- Update documentation and protection script for new naming
- All extensions tested and working correctly

The -ext suffix makes it crystal clear these are extensions and prevents any confusion.

book/config/_quarto-html.yml

@@ -371,14 +371,14 @@ crossref:
       reference-prefix: Video
 
 filters:
-  - ../config/lua/sidenote.lua             # ⚠️ INFO: In HTML, this should not needed.
-  - ../config/lua/inject_parts.lua
-  - ../config/lua/inject_quizzes.lua
+  - filters/sidenote.lua             # ⚠️ INFO: In HTML, this should not needed.
+  - filters/inject_parts.lua
+  - filters/inject_quizzes.lua
   - pandoc-ext/diagram
   # ⚠️ disabled for now because it's not working
-  #- ../config/lua/inject_crossrefs.lua    # ⚠️ WARNING: This must come before custom-numbered-blocks (relies on \ref{...})
-  - mlsysbook/custom-numbered-blocks
-  - ../config/lua/margin-connections.lua   # ⚠️ WARNING: This filter must come after custom-numbered-blocks
+  #- filters/inject_crossrefs.lua    # ⚠️ WARNING: This must come before custom-numbered-blocks (relies on \ref{...})
+  - mlsysbook-ext/custom-numbered-blocks
+  - filters/margin-connections.lua   # ⚠️ WARNING: This filter must come after custom-numbered-blocks
 
 
 # Filter configurations and metadata
@@ -516,7 +516,7 @@ format:
 
     citeproc: true
 
-mlsysbook/custom-numbered-blocks:
+mlsysbook-ext/custom-numbered-blocks:
   groups:
     quiz-question:
       colors: ["F0F0F8", "5B4B8A"]  # Darker purple for quiz questions

book/config/_quarto-pdf.yml

@@ -239,13 +239,13 @@ citation: true
 license: CC-BY-NC-SA
 
 filters:
-  - ../config/lua/sidenote.lua
-  - ../config/lua/inject_parts.lua
-  - ../config/lua/inject_quizzes.lua
+  - ../filters/sidenote.lua
+  - ../filters/inject_parts.lua
+  - ../filters/inject_quizzes.lua
   - pandoc-ext/diagram
-  - ../config/lua/inject_crossrefs.lua    # This must come before custom-numbered-blocks (relies on \ref{...})
-  - mlsysbook/custom-numbered-blocks
-  - ../config/lua/margin-connections.lua  # This filter must come after custom-numbered-blocks
+  - ../filters/inject_crossrefs.lua    # This must come before custom-numbered-blocks (relies on \ref{...})
+  - mlsysbook-ext/custom-numbered-blocks
+  - ../filters/margin-connections.lua  # This filter must come after custom-numbered-blocks
 
   
 # Filter configurations and metadata
@@ -441,7 +441,7 @@ format:
           \usepackage{needspace}
           \let\Needspace\needspace
 
-mlsysbook/custom-numbered-blocks:
+mlsysbook-ext/custom-numbered-blocks:
   groups:
     quiz-question:
       colors: ["F0F0F8", "5B4B8A"]  # Darker purple for quiz questions