diff --git a/.ci/build_docs.sh b/.ci/build_docs.sh
index 71f3ebcb..b8fab375 100755
--- a/.ci/build_docs.sh
+++ b/.ci/build_docs.sh
@@ -44,8 +44,9 @@ GH_REPO_REF="github.com/$GH_REPO_ORG/$GH_REPO_NAME.git"
 
 # Create a clean working directory for this script.
 # Get the current gh-pages branch
-git clone -b gh-pages https://git@$GH_REPO_REF code_docs
-cd code_docs
+cd docs
+git clone -b gh-pages https://git@$GH_REPO_REF html
+cd html
 
 ##### Configure git.
 # Set the push default to simple i.e. push only the current branch.
@@ -71,6 +72,7 @@ echo "" > .nojekyll
 ##### Generate the Doxygen code documentation and log the output.          #####
 echo 'Generating Doxygen code documentation...'
 # Redirect both stderr and stdout to the log file AND the console.
+cd ..
 doxygen $DOXYFILE 2>&1 | tee doxygen.log
 
 ################################################################################
@@ -80,6 +82,7 @@ doxygen $DOXYFILE 2>&1 | tee doxygen.log
 # both exist. This is a good indication that Doxygen did it's work.
 if [ -d "html" ] && [ -f "html/index.html" ]; then
 
+    cd html
     echo 'Uploading documentation to the gh-pages branch...'
     # Add everything in this directory (the Doxygen code documentation) to the
     # gh-pages branch.
diff --git a/docs/Doxyfile b/docs/Doxyfile
index 88c261de..5363a26e 100644
--- a/docs/Doxyfile
+++ b/docs/Doxyfile
@@ -790,7 +790,7 @@ WARN_LOGFILE           =
 # spaces. See also FILE_PATTERNS and EXTENSION_MAPPING
 # Note: If this tag is empty the current directory is searched.
 
-INPUT                  = ../include ../docs/mainpage.md
+INPUT                  = ../include mainpage.md
 
 # This tag can be used to specify the character encoding of the source files
 # that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses
@@ -1111,7 +1111,7 @@ GENERATE_HTML          = YES
 # The default directory is: html.
 # This tag requires that the tag GENERATE_HTML is set to YES.
 
-HTML_OUTPUT            = 
+HTML_OUTPUT            = html
 
 # The HTML_FILE_EXTENSION tag can be used to specify the file extension for each
 # generated HTML page (for example: .htm, .php, .asp).