I regularly use apt to update/upgrade system packages, but i usually forget to update snap packages/apps or github repositories or appimages... For the last one, i haven't found a global solution, but for the others, i did. Below is a simple script, that will update and upgrade your system, based on apt, will update any snap applications and then update all Github repositories in a specified directory. I have also included Flatpak updating, even though i don't use it.

At the end of the process, you will get a nice summary of what went right and what not. If any part of the upgrade has failed, you will get a message at the summary and if any Github repo, failed to make the pull, you will get its name, specifically, to let you know exactly which ones haven't updated. Of course, for the Github repos, they will not build/compile any binaries. They just update the source code. If the repo contains a script you are fine, but if it contains an app, you have to compile it manually, as different programs, demand different ways for building the executable files.

!Make sure to change the directory for the github repos to look for

I also included a line of code, to update pip but i am not going to add any code to update all Python libs, cause it's risky to do so, in one step. If it works... leave it... :) If you have a way to also update any appimages leave a comment.

#!/usr/bin/bash

gtotal=0
gfailed=0
gsuccess=0
update=0
upgrade=0
ssnap=0
sflat=0

rfailed=()

sudo apt update
if [ $? -eq 0 ]; then
    update=0
    sudo apt upgrade
    if [ $? -eq 0 ]; then
      upgrade=0
    else
      upgrade=1
      echo "Failed to upgrade system..."
    fi
  else
    update=1
    echo "Failed to updated repositories... Skipping upgrade."
fi

#update snaps
if [ -x "$(command -v snap)" ]; then
  sudo snap refresh
  if [ $? -eq 0 ]; then
      ssnap=0
    else
      ssnap=1
      echo "Failed to update snap packages."
  fi
fi

#update flatpaks
if [ -x "$(command -v flatpak)" ]; then
  flatpak update
  if [ $? -eq 0 ]; then
      sflat=0
    else
      sflat=1
      echo "Failed to update Flatpak packages."
  fi
fi

#update pip
python3 -m pip install --upgrade pip
if [ $? -eq 0 ]; then
  upip=0
else
  upip=1
fi

#update git repos
for dir in $(find /home/x/apps -name ".git" -type d)
do cd ${dir%/*}
    cd .git
    let "gtotal+=1"
    repo="$(cat config | grep url | cut -d"=" -f2)"
    echo -e "Repository : $repo"
    cd ..
    echo -e "Directory  : $PWD"
    git pull
    if [ $? -eq 0 ]; then
      echo "Succesful updated repo: $repo"
      let "gsuccess+=1"
    else
      echo "Failed... $repo"
      rfailed+=($repo)
      let "gfailed+=1"
    fi
    echo ""
    cd - > /dev/null
done

echo "## Summary #########################"
echo ""
echo "-- System --------------------------"
if [ $update -eq 0 ]; then
    echo "Successful updated repositories."
  else
    echo "Failed to update repositories!"
fi
if [ $upgrade -eq 0 ]; then
    echo "Successful upgraded system."
  else
    echo "Failed to upgrade system!"
fi

echo ""
echo "-- Python --------------------------"
if [ $upip -eq 0 ]; then
  echo "PIP updated."
else
  echo "Failed to Updated PIP!"
fi

if [ -x "$(command -v snap)" ]; then
  echo ""
  echo "-- Snaps ---------------------------"
  if [ $ssnap -eq 0 ]; then
      echo "Successful upgraded Snap packages."
    else
      echo "Failed to upgrade Snap packages!"
  fi
fi

if [ -x "$(command -v flatpak)" ]; then
  echo ""
  echo "-- Snaps ---------------------------"
  if [ $sflat -eq 0 ]; then
      echo "Successful upgraded Flatpak packages."
    else
      echo "Failed to upgrade Flatpak packages!"
  fi
fi

echo ""
echo "-- GitHub --------------------------"
echo "Total Repositories: $gtotal"
echo "Failed to update: $gfailed"
echo "Succesful updated: $gsuccess"

if [ ! $gfailed -eq 0 ]; then
  echo ""
  echo "Failed GitHub repositories:"
  printf "%s\n" "${rfailed[@]}"
fi

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