diff --git a/.github/workflows/gen-docs.yaml b/.github/workflows/gen-docs.yaml
index 418aa1c745..ac0fdee457 100644
--- a/.github/workflows/gen-docs.yaml
+++ b/.github/workflows/gen-docs.yaml
@@ -14,13 +14,13 @@ jobs:
         submodules: recursive
         fetch-depth: 0
 
-    - name: Install ncftp, kicad, doxygen, and yq
+    - name: Install ncftp, kicad, doxygen, graphviz, and yq
       run: |
         sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys CC86BB64
         sudo add-apt-repository ppa:rmescandon/yq
         sudo add-apt-repository ppa:kicad/kicad-5.1-releases
         sudo apt-get update
-        sudo apt-get install ncftp kicad doxygen yq
+        sudo apt-get install ncftp kicad doxygen graphviz yq
 
     - name: Set FTP variables
       env:
diff --git a/firmware/Doxyfile b/firmware/Doxyfile
index 663109fe00..ce5c03bab0 100644
--- a/firmware/Doxyfile
+++ b/firmware/Doxyfile
@@ -780,7 +780,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                =
+EXCLUDE                = ./ChibiOS ./ChibiOS-Contrib ./config/boards/hellen/cypress/OS
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded
diff --git a/misc/jenkins/generate_doxygen/gen_upload_docs.sh b/misc/jenkins/generate_doxygen/gen_upload_docs.sh
index c4daf685e2..06fa1e8ef4 100644
--- a/misc/jenkins/generate_doxygen/gen_upload_docs.sh
+++ b/misc/jenkins/generate_doxygen/gen_upload_docs.sh
@@ -20,7 +20,7 @@ doxygen || { echo "doxygen run FAILED"; exit 1; }
 cd ../doxygen
 if [ -n "$RUSEFI_FTP_SERVER" ]; then
   echo "Uploading Doxygen"
-  ncftpput -R -m -u "$RUSEFI_DOXYGEN_FTP_USER" -p "$RUSEFI_DOXYGEN_FTP_PASS" "$RUSEFI_FTP_SERVER" /html html/
+  ncftpput -R -m -u "$RUSEFI_DOXYGEN_FTP_USER" -p "$RUSEFI_DOXYGEN_FTP_PASS" "$RUSEFI_FTP_SERVER" /html html/*
 fi
 [ $? -eq 0 ] || { echo "upload FAILED"; exit 1; }
 
@@ -48,6 +48,6 @@ done
 
 if [ -n "$RUSEFI_FTP_SERVER" ]; then
   echo "Uploading Pinouts"
-  ncftpput -R -m -u "$RUSEFI_DOXYGEN_FTP_USER" -p "$RUSEFI_DOXYGEN_FTP_PASS" "$RUSEFI_FTP_SERVER" /pinouts pinouts/
+  ncftpput -R -m -u "$RUSEFI_DOXYGEN_FTP_USER" -p "$RUSEFI_DOXYGEN_FTP_PASS" "$RUSEFI_FTP_SERVER" /pinouts pinouts/*
 fi
 [ $? -eq 0 ] || { echo "upload FAILED"; exit 1; }