diff --git a/.github/workflows/cygwin_build.yml b/.github/workflows/cygwin_build.yml
index 39b1051577526..13deb38db496f 100644
--- a/.github/workflows/cygwin_build.yml
+++ b/.github/workflows/cygwin_build.yml
@@ -187,9 +187,8 @@ jobs:
           PATH: /usr/bin:$(cygpath ${SYSTEMROOT})/system32
         shell: C:\cygwin\bin\bash.exe -eo pipefail '{0}'
         run: >-
-          ln -sf /usr/bin/python3.7 /usr/bin/python && ln -sf /usr/bin/pip3.7 /usr/bin/pip &&
-          python -m pip install --progress-bar off empy==3.3.4 pexpect &&
-          python -m pip install --progress-bar off dronecan --upgrade &&
+          python3 -m pip install --progress-bar off empy==3.3.4 pexpect &&
+          python3 -m pip install --progress-bar off dronecan --upgrade &&
           cp /usr/bin/ccache /usr/local/bin/ &&
           cd /usr/local/bin && ln -s ccache /usr/local/bin/gcc &&
           ln -s ccache /usr/local/bin/g++ &&
diff --git a/.github/workflows/esp32_build.yml b/.github/workflows/esp32_build.yml
index d503ca6ca9498..a8c97e0badd06 100644
--- a/.github/workflows/esp32_build.yml
+++ b/.github/workflows/esp32_build.yml
@@ -176,9 +176,7 @@ jobs:
         run: |
           sudo apt-get update
           sudo apt-get install git wget libncurses-dev flex bison gperf python3 python3-pip python3-venv python3-setuptools python3-serial python3-gevent python3-cryptography python3-future python3-pyparsing python3-pyelftools cmake ninja-build ccache libffi-dev libssl-dev dfu-util libusb-1.0-0
-          sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10
-          update-alternatives --query python
-          python --version
+          python3 --version
           pip3 install gevent
 
           # we actualy want 3.11 .. but the above only gave us 3.10, not ok with esp32 builds.
@@ -186,13 +184,10 @@ jobs:
           sudo apt-get update
           sudo apt-get install python3.11 python3.11-venv python3.11-distutils  -y
           sudo apt-get install python3 python3-pip python3-venv python3-setuptools python3-serial python3-cryptography python3-future python3-pyparsing python3-pyelftools
-          update-alternatives --query python
           pip3 install gevent
-          python --version
+          python3 --version
           python3.11 --version
           which python3.11
-          sudo update-alternatives --install /usr/bin/python python /usr/bin/python3.11 11
-          update-alternatives --query python
 
           rm -rf /usr/local/bin/cmake
           sudo apt-get remove --purge --auto-remove cmake
@@ -229,7 +224,7 @@ jobs:
           ./install.sh
           source ./export.sh
           cd ../..
-          python -m pip install --progress-bar off future lxml pymavlink MAVProxy pexpect flake8 geocoder empy==3.3.4 dronecan
+          python3 -m pip install --progress-bar off future lxml pymavlink MAVProxy pexpect flake8 geocoder empy==3.3.4 dronecan
           which cmake
           ./waf configure --board ${{matrix.config}} 
           echo './waf configure --board ${{matrix.config}}' >> $GITHUB_STEP_SUMMARY  
diff --git a/Tools/autotest/bisect-helper.py b/Tools/autotest/bisect-helper.py
index 3858a53fb6b3a..90f74dec69ed1 100755
--- a/Tools/autotest/bisect-helper.py
+++ b/Tools/autotest/bisect-helper.py
@@ -1,4 +1,4 @@
-#!/usr/bin/env python
+#!/usr/bin/env python3
 
 '''A helper script for bisecting common problems when working with ArduPilot
 
diff --git a/Tools/environment_install/install-prereqs-alpine.sh b/Tools/environment_install/install-prereqs-alpine.sh
index c01da408db3ef..5f1dd9af6e602 100755
--- a/Tools/environment_install/install-prereqs-alpine.sh
+++ b/Tools/environment_install/install-prereqs-alpine.sh
@@ -17,7 +17,6 @@ apk update && apk add --no-cache \
         libxml2-dev \
         libxslt-dev \
         git \
-    && ln -sf python3 /usr/bin/python \
     &&  rm -rf /var/cache/apk/*
 
 python3 -m pip install --user --no-deps --no-cache-dir empy==3.3.4 pexpect ptyprocess --break-system-packages
diff --git a/Tools/environment_install/install-prereqs-windows-andAPMSource.ps1 b/Tools/environment_install/install-prereqs-windows-andAPMSource.ps1
index 2076ce1f588d6..7a92147fb74af 100644
--- a/Tools/environment_install/install-prereqs-windows-andAPMSource.ps1
+++ b/Tools/environment_install/install-prereqs-windows-andAPMSource.ps1
@@ -15,11 +15,9 @@ Start-BitsTransfer -Source "https://firmware.ardupilot.org/Tools/STM32-tools/gcc
 
 Write-Output "Installing Cygwin x64 (4/8)"
 Start-Process -wait -FilePath $PSScriptRoot\setup-x86_64.exe -ArgumentList "--root=C:\cygwin64 --no-startmenu --local-package-dir=$env:USERPROFILE\Downloads --site=http://cygwin.mirror.constant.com --packages autoconf,automake,ccache,cygwin32-gcc-g++,gcc-g++=7.4.0-1,libgcc1=7.4.0.1,gcc-core=7.4.0-1,git,libtool,make,gawk,libexpat-devel,libxml2-devel,python37,python37-future,python37-lxml,python37-pip,libxslt-devel,python37-devel,procps-ng,zip,gdb,ddd --quiet-mode"
-Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'ln -sf /usr/bin/python3.7 /usr/bin/python'"
-Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'ln -sf /usr/bin/pip3.7 /usr/bin/pip'"
 
 Write-Output "Downloading extra Python packages (5/8)"
-Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'pip install empy==3.3.4 pyserial pymavlink intelhex dronecan pexpect'"
+Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'pip3 install empy==3.3.4 pyserial pymavlink intelhex dronecan pexpect'"
 
 Write-Output "Downloading APM source (6/8)"
 Copy-Item "APM_install.sh" -Destination "C:\cygwin64\home"
diff --git a/Tools/environment_install/install-prereqs-windows.ps1 b/Tools/environment_install/install-prereqs-windows.ps1
index 15bac628949e8..17d99bf86408b 100644
--- a/Tools/environment_install/install-prereqs-windows.ps1
+++ b/Tools/environment_install/install-prereqs-windows.ps1
@@ -15,11 +15,9 @@ Start-BitsTransfer -Source "https://firmware.ardupilot.org/Tools/STM32-tools/gcc
 
 Write-Output "Installing Cygwin x64 (4/7)"
 Start-Process -wait -FilePath $PSScriptRoot\setup-x86_64.exe -ArgumentList "--root=C:\cygwin64 --no-startmenu --local-package-dir=$env:USERPROFILE\Downloads --site=http://cygwin.mirror.constant.com --packages autoconf,automake,ccache,cygwin32-gcc-g++,gcc-g++=7.4.0-1,libgcc1=7.4.0.1,gcc-core=7.4.0-1,git,libtool,make,gawk,libexpat-devel,libxml2-devel,python37,python37-future,python37-lxml,python37-pip,libxslt-devel,python37-devel,procps-ng,zip,gdb,ddd,xterm --quiet-mode"
-Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'ln -sf /usr/bin/python3.7 /usr/bin/python'"
-Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'ln -sf /usr/bin/pip3.7 /usr/bin/pip'"
 
 Write-Output "Downloading extra Python packages (5/7)"
-Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'pip install empy==3.3.4 pyserial pymavlink intelhex dronecan pexpect'"
+Start-Process -wait -FilePath "C:\cygwin64\bin\bash" -ArgumentList "--login -i -c 'pip3 install empy==3.3.4 pyserial pymavlink intelhex dronecan pexpect'"
 
 Write-Output "Installing ARM GCC Compiler 10-2020-Q4-Major (6/7)"
 & $PSScriptRoot\gcc-arm-none-eabi-10-2020-q4-major-win32.exe /S /P /R
diff --git a/Tools/scripts/build_appveyor.sh b/Tools/scripts/build_appveyor.sh
index d392bbe4e041d..e06ef2591ac52 100755
--- a/Tools/scripts/build_appveyor.sh
+++ b/Tools/scripts/build_appveyor.sh
@@ -18,7 +18,7 @@ cd /cygdrive/c/work
 
     ./waf configure --board sitl
 
-    /usr/bin/python waf -j4 copter plane rover heli sub
+    python3 waf -j4 copter plane rover heli sub
 
     # map to the names that MissionPlanner expects
     cp /cygdrive/c/work/build/sitl/bin/ardurover.exe /cygdrive/c/work/sitl/Rover.elf
diff --git a/Tools/scripts/filter_size_compare_branches_csv.py b/Tools/scripts/filter_size_compare_branches_csv.py
index 8030608c5e747..aa42fa2a097dc 100755
--- a/Tools/scripts/filter_size_compare_branches_csv.py
+++ b/Tools/scripts/filter_size_compare_branches_csv.py
@@ -1,4 +1,4 @@
-#!/usr/bin/python
+#!/usr/bin/env python3
 
 import argparse
 import csv
diff --git a/libraries/AP_HAL_ESP32/README.md b/libraries/AP_HAL_ESP32/README.md
index cfd829fcde766..6c35ea692e504 100644
--- a/libraries/AP_HAL_ESP32/README.md
+++ b/libraries/AP_HAL_ESP32/README.md
@@ -20,7 +20,6 @@ Tools/environment_install/install-prereqs-arch.sh
 # from: https://docs.espressif.com/projects/esp-idf/en/latest/esp32/get-started/linux-setup.html
 sudo apt-get install git wget flex bison gperf cmake ninja-build ccache libffi-dev libssl-dev dfu-util
 sudo apt-get install python3 python3-pip python3-setuptools
-sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 10
 
 #or
 sudo pacman -S --needed gcc git make flex bison gperf python-pip cmake ninja ccache dfu-util libusb
diff --git a/modules/waf b/modules/waf
index b25b5c7d98c50..5b5436e0c57e9 160000
--- a/modules/waf
+++ b/modules/waf
@@ -1 +1 @@
-Subproject commit b25b5c7d98c502b07976740b0a65b9f39948c292
+Subproject commit 5b5436e0c57e9a587ed69a33443e7b6543201266