diff --git a/.gitignore b/.gitignore
index 8cc1778fd..4299c9af1 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,21 +1,23 @@
-build/
-build_autotests/
-.pio/
+!.gitignore
+
+# OS
 install
-source/config/*
+.DS_Store
 *.app
 *.desktop
 *.user
 *.log
-!.gitignore
 
-#IDE
-software/controller/CMakeLists*
-software/common/CMakeLists*
-cmake-build-*/
-.idea/
+# IDE: VSCode
+.vscode
+
+# IDE: JetBrains
 .idea
-.vscode/
+.idea/
+CMakeLists.txt.user
+cmake-build-*/
+
+# IDE: other
 .ctags
 ctags
 tags
@@ -23,35 +25,13 @@ tags
 cscope.out
 *~
 
-#CAD/Inventor
-*.lck
-OldVersions/
-
-.DS_Store
 .clangd/
 .*.swp
 *.map
 last_graph.dat
 
-coverage_reports
-
-# KiCAD backups
-*.sch-bak
-*.kicad_pcb-bak
-*.bak
-# KiCAD temp/unneeded cache files
-_autosave-*
-*.000
-fp-info-cache
-# (project symbol cache library not needed as all symbols kept in RespiraWorks libraries)
-*-cache.lib
-
 #performance test data
 local_data/
-test_data/
-
-#Conan created files
-CMakeUserPresets.json
 
 # Byte-compiled / optimized / DLL files
 __pycache__/
diff --git a/docs/docs.sh b/docs/docs.sh
index f99264c7e..25d9acf80 100755
--- a/docs/docs.sh
+++ b/docs/docs.sh
@@ -46,10 +46,14 @@ install_linux() {
   install_py
   sudo apt update
   sudo apt --yes install \
-           make \
-           doxygen \
-           graphviz
-  sudo apt --yes install apt-transport-https ca-certificates curl software-properties-common
+       make \
+       doxygen \
+       graphviz
+  sudo apt --yes install \
+       apt-transport-https \
+       ca-certificates \
+       curl \
+       software-properties-common
   curl -fsSL https://download.docker.com/linux/ubuntu/gpg \
     | sudo gpg --dearmor -o /usr/share/keyrings/docker-archive-keyring.gpg
   echo "deb [arch=$(dpkg --print-architecture) signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/ubuntu $(lsb_release -cs) stable" \
@@ -86,7 +90,7 @@ launch_browser() {
 
 check_links() {
   echo "If you wish to use \`./docs.sh check\` to check validity of links locally, please follow installation instructions at https://github.com/lycheeverse/lychee"
-  docker run --init --rm -w /input -v "$(pwd)/..":/input lycheeverse/lychee -c ./docs/lychee.toml .
+  docker run --init --rm -w /input -v "$(pwd)/..":/input lycheeverse/lychee -c ./docs/lychee.toml --no-ignore .
 #  lychee ..
 }
 
diff --git a/docs/lychee.toml b/docs/lychee.toml
index 2abae7b89..48be949d3 100644
--- a/docs/lychee.toml
+++ b/docs/lychee.toml
@@ -92,15 +92,15 @@ exclude = [
     '.*\.valispace.com\.*',
     '.*\wonsmart-motor.en.made-in-china.com\.*',
     '.*\.raspberrypi.com\.*',
-    '.*\.servoflo.com\.*'
+    '.*\.servoflo.com\.*',
+    '.*\.rawgit.com\.*',
 ]
 
 # Exclude these filesystem paths from getting checked.
 exclude_path = [
-    "../software/common/coverage_reports",
-    "../software/controller/coverage_reports",
-    "../software/gui/coverage_reports",
-    "../software/gui/src/third_party"
+    "software/common/coverage_reports",
+    "software/controller/coverage_reports",
+    "software/gui/coverage_reports",
 ]
 
 # Exclude all private IPs from checking.
diff --git a/manufacturing/.gitignore b/manufacturing/.gitignore
new file mode 100644
index 000000000..73e7b7427
--- /dev/null
+++ b/manufacturing/.gitignore
@@ -0,0 +1,3 @@
+#CAD/Inventor
+*.lck
+OldVersions/
diff --git a/pcb/.gitignore b/pcb/.gitignore
new file mode 100644
index 000000000..fde52511b
--- /dev/null
+++ b/pcb/.gitignore
@@ -0,0 +1,10 @@
+# KiCAD backups
+*.sch-bak
+*.kicad_pcb-bak
+*.bak
+# KiCAD temp/unneeded cache files
+_autosave-*
+*.000
+fp-info-cache
+# (project symbol cache library not needed as all symbols kept in RespiraWorks libraries)
+*-cache.lib
diff --git a/software/common/.gitignore b/software/common/.gitignore
index 0ba5c61b2..d891eccad 100644
--- a/software/common/.gitignore
+++ b/software/common/.gitignore
@@ -1,3 +1,5 @@
 #network protocol output files
 generated_libs/protocols/*.c
 generated_libs/protocols/*.h
+.pio/
+coverage_reports/
diff --git a/software/common/common.sh b/software/common/common.sh
index 090694dc3..d63a19f05 100755
--- a/software/common/common.sh
+++ b/software/common/common.sh
@@ -78,7 +78,7 @@ generate_network_protocols() {
   mkdir -p "$PYTHON_LIB_PATH"
   mkdir -p "$GUI_LIB_PATH"
   #ensure old files are gone
-  rm -f $PROTOCOLS_DIR/*.h $PROTOCOLS_DIR/*.c $GUI_LIB_PATH/*.c* $GUI_LIB_PATH/*.h* $PYTHON_LIB_PATH/*.py
+  rm -f $PROTOCOLS_DIR/*.h $PROTOCOLS_DIR/*.c $GUI_LIB_PATH/*.c* $GUI_LIB_PATH/*.h* $PYTHON_LIB_PATH/*_pb2.py
 
   protoc \
   --plugin="$NANOPB_PLUGIN" \
diff --git a/software/controller/.gitignore b/software/controller/.gitignore
new file mode 100644
index 000000000..29b0d215b
--- /dev/null
+++ b/software/controller/.gitignore
@@ -0,0 +1,2 @@
+.pio/
+coverage_reports/
diff --git a/software/controller/controller.sh b/software/controller/controller.sh
index 6ec9970b7..6c97c218f 100755
--- a/software/controller/controller.sh
+++ b/software/controller/controller.sh
@@ -329,6 +329,9 @@ elif [ "$1" == "check" ]; then
 elif [ "$1" == "unit" ]; then
   clean_all
 
+  # generate comms protocols
+  ../common/common.sh generate
+
   if [ -n "$2" ]; then
     pio test -e native -f "$2"
   else
diff --git a/software/gui/.gitignore b/software/gui/.gitignore
index 58f325f1b..1d106f4c0 100644
--- a/software/gui/.gitignore
+++ b/software/gui/.gitignore
@@ -1,3 +1,8 @@
 #network protocol output files
 src/protocols/*.cc
 src/protocols/*.h
+build/
+coverage_reports/
+
+#Conan created files
+CMakeUserPresets.json
diff --git a/software/gui/gui.sh b/software/gui/gui.sh
index 3137923d3..c4b6d14bd 100755
--- a/software/gui/gui.sh
+++ b/software/gui/gui.sh
@@ -195,7 +195,6 @@ elif [ "$1" == "build" ]; then
   ensure_not_root
 
   # generate comms protocols
-  ../common/common.sh update
   ../common/common.sh generate
 
   config_type="Release"
@@ -253,7 +252,6 @@ elif [ "$1" == "test" ]; then
   ensure_not_root
 
   # generate comms protocols
-  ../common/common.sh update
   ../common/common.sh generate
 
   j_opt=""