Update mathjax cdn, fix header links, and clean up web gen script

Author: itslevismith

gen-website

@@ -9,23 +9,20 @@ cmake -DCMAKE_INSTALL_PREFIX=/opt/biogears/usr -DBiogears_BUILD_WEBSITE=ON -DBio
 cd runtime
 
 echo "Finished building BioGears"
-sleep 5
 
 if [ "${GENSTATES}" == "true" ]; then
     echo "Running cmd_bio GENSTATES ..."
     ../outputs/Release/bin/cmd_bio GENSTATES
 fi
 
 echo "Passed GENSTATES"
-sleep 5
 
 if [ "${VALIDATE}" == "true" ]; then
     echo "Running cmd_bio VALIDATE all ..."
     ../outputs/Release/bin/cmd_bio VALIDATE all
 fi
 
 echo "Passed VALIDATE"
-sleep 5
 
 # Only run if starting from a clean build of BioGears... running and validating everything from scratch
 
@@ -34,25 +31,21 @@ echo "Running cmd_bio GENTABLES ..."
 ../outputs/Release/bin/cmd_bio GENTABLES all
 
 echo "Passed GENTABLES"
-sleep 5
 
 # Copy non-regenerated files from share/website into runtime and reorganizes files in runtime+
 python3 ../../share/website/WebsiteGenerationPreProcess.py /opt/biogears/core/share/website /opt/biogears/core/build/runtime
 
 echo "Passed WebGenPreProcess"
-sleep 5
 
 # Preprocess MD files for website generation and create graphs
 cmake --build .. --target docs-prepare
 
 echo "Passed docs-prepare"
-sleep 5
 
 # Run Doxygen
 cmake --build .. --target docs-doxygen
 
 echo "Passed docs-doxygen"
-sleep 5
 
 # Copy files into documentation folder
 cmake --build .. --target docs-stage

share/doc/doxygen/doxyfile.in

@@ -1486,7 +1486,7 @@ MATHJAX_FORMAT         = HTML-CSS
 # The default value is: http://cdn.mathjax.org/mathjax/latest.
 # This tag requires that the tag USE_MATHJAX is set to YES.
 
-MATHJAX_RELPATH        = http://cdn.mathjax.org/mathjax/latest
+MATHJAX_RELPATH        = https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.7/MathJax.js
 
 # The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax
 # extension names that should be enabled during MathJax rendering. For example

share/doc/doxygen/header.html

@@ -43,8 +43,8 @@
                     <span class="icon-bar"></span>
                     <span class="icon-bar"></span>
                 </button>
-                <a class="navbar-brand hidden-sm" href="./"><img style='margin-top: -8px !important;height: 40px !important;' src='./images/biogears_logoWT.png' /></a>
-                <a class="navbar-brand visible-sm" style='margin-left: -30px !important;width: 60px !important;' href="./"><img style='margin-top: -10px !important;height: 40px !important;' src='./images/bg_symbolWT.png' /></a>
+                <a class="navbar-brand hidden-sm" href="/"><img style='margin-top: -8px !important;height: 40px !important;' src='./images/biogears_logoWT.png' /></a>
+                <a class="navbar-brand visible-sm" style='margin-left: -30px !important;width: 60px !important;' href="/"><img style='margin-top: -10px !important;height: 40px !important;' src='./images/bg_symbolWT.png' /></a>
             </div>
             <div class="collapse navbar-collapse">
                 <!-- Left -->