fix update

.gitignore

@@ -0,0 +1 @@
+gnome/.gnome-settings.md5

bitwarden.sh

@@ -1,6 +1,6 @@
 #!/bin/bash
 
-export SSH_AUTH_SOCK="$HOME/.bitwarden-ssh-agent.sock"
+LINE='export SSH_AUTH_SOCK="$HOME/.bitwarden-ssh-agent.sock"'
 
 if grep -qF "$LINE" ~/.bashrc; then
   echo "Bitwarden SSH agent already configured in .bashrc"

gnome/apply-gnome-settings.sh

@@ -0,0 +1,24 @@
+#!/bin/bash
+#
+# Purpose : Apply gnome-settings.dconf only if it has changed since last applied
+#           (tracked via an MD5 checksum so user tweaks aren't overwritten every run)
+
+SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
+SRC="$SCRIPT_DIR/gnome-settings.dconf"
+CHECKSUM_FILE="$SCRIPT_DIR/.gnome-settings.md5"
+
+if [ ! -f "$SRC" ]; then
+  echo "Error: $SRC not found."
+  exit 1
+fi
+
+CURRENT_SUM=$(md5sum "$SRC" | awk '{print $1}')
+STORED_SUM=$(cat "$CHECKSUM_FILE" 2>/dev/null)
+
+if [ "$CURRENT_SUM" != "$STORED_SUM" ]; then
+  echo "GNOME settings have changed, applying..."
+  dconf load /org/gnome/shell/extensions/ < "$SRC"
+  echo "$CURRENT_SUM" > "$CHECKSUM_FILE"
+else
+  echo "GNOME settings unchanged, skipping."
+fi

gnome/gnome-settings.sh

@@ -2,6 +2,5 @@
 SCRIPT_DIR="$( cd "$( dirname "${BASH_SOURCE[0]}" )" && pwd )"
 
 gsettings set org.gnome.desktop.interface gtk-theme "Adwaita-dark"
-echo "setting wallpaper to ${SCRIPT_DIR}/wallpaper.jpeg"
 gsettings set org.gnome.desktop.background picture-uri-dark "file://${SCRIPT_DIR}/wallpaper.jpeg"
 gsettings set org.gnome.desktop.background picture-options 'zoom'

install.sh

@@ -105,9 +105,6 @@ install_packages "${MAINTENANCE[@]}"
 echo "Installing desktop environment..."
 install_packages "${DESKTOP[@]}"
 
-echo "Installing office packages..."
-install_packages "${OFFICE[@]}"
-
 echo "Installing media packages..."
 install_packages "${MEDIA[@]}"
 
@@ -117,14 +114,7 @@ install_packages "${FONTS[@]}"
 # Enable all systemd services listed in SERVICES array, then register the SSH
 # Avahi service so the machine is discoverable over mDNS
 echo "Configuring services..."
-for service in "${SERVICES[@]}"; do
-  if ! systemctl is-enabled "$service" &> /dev/null; then
-    echo "Enabling $service..."
-    sudo systemctl enable "$service"
-  else
-    echo "$service is already enabled."
-  fi
-done
+enable_services "${SERVICES[@]}"
 sudo cp /usr/share/doc/avahi/ssh.service /etc/avahi/services/
 
 cd ~/.local/share/coredesktop
@@ -178,31 +168,7 @@ if ! systemctl is-active tailscaled &> /dev/null; then
 fi
 
 # Apply GNOME dconf settings only if the settings file has changed since last run
-# (tracked via an MD5 checksum to avoid redundant writes)
-SRC="$HOME/.local/share/coredesktop/gnome/gnome-settings.dconf"
-CHECKSUM_FILE="$HOME/.local/share/coredesktop/gnome/.gnome-settings.md5"
-
-if [ ! -f "$SRC" ]; then
-  echo "Error: $SRC not found, exiting."
-  exit 1
-fi
-
-CURRENT_SUM=$(md5sum "$SRC" | awk '{print $1}')
-
-if [ -f "$CHECKSUM_FILE" ]; then
-  STORED_SUM=$(cat "$CHECKSUM_FILE")
-else
-  STORED_SUM=""
-fi
-
-if [ "$CURRENT_SUM" != "$STORED_SUM" ]; then
-  echo "GNOME settings have changed, applying..."
-  dconf load /org/gnome/shell/extensions/ < "$SRC"
-  echo "$CURRENT_SUM" > "$CHECKSUM_FILE"
-  echo "Done."
-else
-  echo "GNOME settings unchanged, skipping."
-fi
+bash ~/.local/share/coredesktop/gnome/apply-gnome-settings.sh
 
 # Fix mDNS configuration if systemd-resolved is managing DNS on this system
 if systemctl is-enabled systemd-resolved.service &> /dev/null; then

packages.conf

@@ -96,6 +96,7 @@ MAINTENANCE=(
   gnome-disk-utility
   gnome-extra
   gnome-keyring
+  pacman-contrib
 )
 
 # Desktop environment
@@ -134,6 +135,7 @@ SERVICES=(
   avahi-daemon.service
   bluetooth.service
   cups.service
+  fwupd-refresh.timer
   gdm.service
   NetworkManager.service
   sshd.service

skills/sibling-project-updates.md

@@ -12,10 +12,12 @@ during its own install step.
 When a user runs `update`:
 
 1. The coredesktop repo at `~/.local/share/coredesktop` is pulled.
-2. All `*.sh` files in `updates.d/` are **sourced** (not executed as subprocesses)
+2. All `*.sh` files in `updates.d/` are **sourced**, each in its own subshell,
    in lexicographic order.
-3. Each script runs in the same shell context, with access to `$COREDESKTOP` and
-   anything sourced before it (e.g. `utils.sh`).
+3. Each script can see `$COREDESKTOP`, but nothing defined by earlier hooks —
+   source `utils.sh` yourself if you need its helpers. A `cd`, `set -e` or `exit`
+   in one hook can't affect the others.
+4. A hook that exits non-zero is listed in the summary at the end of `update`.
 
 Because the scripts are sourced from within the cloned repo directory, any file
 placed there by a sibling project's installer will **survive `git pull`** — git
@@ -26,16 +28,27 @@ does not delete untracked files on pull.
 Existing coredesktop hooks use a numeric prefix to control execution order:
 
 | File                      | Purpose                                 |
-|------------------|---------------------|
+|---------------------------|-----------------------------------------|
+| `00-rename-migration.sh`  | Legacy command renames                  |
 | `10-pacman.sh`            | Arch system update                      |
+| `15-services.sh`          | Enable new systemd services             |
 | `20-aur.sh`               | AUR packages                            |
 | `30-flatpak.sh`           | Flatpak apps                            |
-| `40-ruby.sh`     | Ruby/gems           |
-| `50-bitwarden.sh`| Bitwarden CLI       |
+| `40-ruby.sh`              | mise, Ruby/gems                         |
+| `45-tmux.sh`              | TPM and tmux plugins                    |
+| `46-neovim.sh`            | Neovim plugins                          |
+| `50-bitwarden.sh`         | Bitwarden SSH agent                     |
 | `60-pipx.sh`              | pipx packages                           |
+| `65-migrate.sh`           | Migrate backup tool                     |
+| `70-claude.sh`            | Claude Code setup                       |
+| `80-gnome-extensions.sh`  | GNOME extensions                        |
+| `85-gnome-settings.sh`    | GNOME extension settings                |
+| `90-firmware.sh`          | Firmware update check                   |
+| `95-cleanup.sh`           | Flatpak/pacman cache cleanup            |
+| `99-reboot-check.sh`      | Reboot-needed notice                    |
 
-Sibling projects should use **70 or higher** to run after all coredesktop
-updates complete.
+Sibling projects should use an unused number from **71–79** so they run after
+the core updates but before coredesktop's end-of-run hooks (80+).
 
 ## What to Add to a Sibling Project
 
@@ -68,8 +81,9 @@ run on the machine.
 
 ## Available Helpers
 
-Since hooks are sourced in the same shell, they can use any function or variable
-already defined by earlier scripts. The most useful are in `utils.sh`:
+Hooks don't inherit functions from earlier hooks, so source `utils.sh` for its
+helpers. Do this before defining your own `is_installed`, because `utils.sh` has
+a pacman-specific function with the same name:
 
 ```bash
 source "$COREDESKTOP/utils.sh"
@@ -86,5 +100,5 @@ remove_packages "${MY_REMOVE_PACKAGES[@]}"
 - [ ] Create `updates.d/7X-<project>.sh` in the sibling repo
 - [ ] Hook script echoes its name so progress is visible during `update`
 - [ ] Install step copies the hook to `~/.local/share/coredesktop/updates.d/`
-- [ ] Numeric prefix is 70+ (does not conflict with coredesktop's own hooks)
+- [ ] Numeric prefix is an unused number in 71–79
 - [ ] Script is idempotent — safe to run multiple times without side effects

update

@@ -23,18 +23,28 @@ print_logo
 COREDESKTOP="$HOME/.local/share/coredesktop"
 
 echo "Updating CoreDesktop..."
-git -C "$COREDESKTOP" pull
+if [[ -z "$UPDATE_REEXECED" ]] && ! git -C "$COREDESKTOP" pull; then
+    echo "WARNING: could not pull the latest CoreDesktop; running the update hooks already on disk."
+    export UPDATE_PULL_FAILED=1
+fi
 mkdir -p "$COREDESKTOP/updates.d"
-sudo cp "$COREDESKTOP/update" ~/.local/bin/update
-sudo cp "$COREDESKTOP/refresh" ~/.local/bin/refresh
+# --remove-destination replaces copies left root-owned by older versions of this script
+cp --remove-destination "$COREDESKTOP/update" ~/.local/bin/update
+cp --remove-destination "$COREDESKTOP/refresh" ~/.local/bin/refresh
 
 if [[ -z "$UPDATE_REEXECED" ]]; then
     export UPDATE_REEXECED=1
     exec ~/.local/bin/update
 fi
 
+FAILED=()
+[[ -n "$UPDATE_PULL_FAILED" ]] && FAILED+=("git pull")
+
+# Each hook runs in its own subshell so a cd, set -e, exit, or stray variable
+# in one hook can't leak into or abort the hooks after it.
 for plugin in "$COREDESKTOP/updates.d/"*.sh; do
-    if [ -f "$plugin" ]; then
+    [ -f "$plugin" ] || continue
+    (
         unset -f is_installed run_update
         source "$plugin"
         if declare -f run_update > /dev/null; then
@@ -42,7 +52,14 @@ for plugin in "$COREDESKTOP/updates.d/"*.sh; do
                 run_update
             fi
         fi
-    fi
+    )
+    # Checked separately: under `( ... ) ||`, bash would ignore set -e inside the hook
+    [ $? -eq 0 ] || FAILED+=("$(basename "$plugin")")
 done
 
+if (( ${#FAILED[@]} > 0 )); then
+    echo "Done, with errors in: ${FAILED[*]}"
+    exit 1
+fi
+
 echo "Done."

updates.d/00-rename-migration.sh

@@ -4,12 +4,12 @@ COREDESKTOP="$HOME/.local/share/coredesktop"
 
 if [ -f ~/.local/bin/coreupdate ]; then
     echo "Migrating coreupdate -> update..."
-    sudo cp "$COREDESKTOP/update" ~/.local/bin/update
+    cp --remove-destination "$COREDESKTOP/update" ~/.local/bin/update
     sudo rm -f ~/.local/bin/coreupdate
 fi
 
 if [ -f ~/.local/bin/corerefresh ]; then
     echo "Migrating corerefresh -> refresh..."
-    sudo cp "$COREDESKTOP/refresh" ~/.local/bin/refresh
+    cp --remove-destination "$COREDESKTOP/refresh" ~/.local/bin/refresh
     sudo rm -f ~/.local/bin/corerefresh
 fi

updates.d/15-services.sh

@@ -0,0 +1,9 @@
+#!/bin/bash
+
+COREDESKTOP="$HOME/.local/share/coredesktop"
+
+source "$COREDESKTOP/utils.sh"
+source "$COREDESKTOP/packages.conf"
+
+echo "Checking for new services..."
+enable_services "${SERVICES[@]}"

updates.d/40-ruby.sh

@@ -1,5 +1,8 @@
 #!/bin/bash
 
+echo "Updating mise..."
+mise self-update -y
+
 echo "Updating Ruby and Rails..."
 mise upgrade --bump ruby
 mise reshim

updates.d/45-tmux.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+is_installed() {
+  [ -d "$HOME/.tmux/plugins/tpm" ]
+}
+
+run_update() {
+  echo "Updating TPM and tmux plugins..."
+  local failed=0
+  for plugin in "$HOME/.tmux/plugins/"*/; do
+    [ -d "$plugin/.git" ] || continue
+    echo "  $(basename "$plugin")"
+    git -C "$plugin" pull --ff-only --quiet || failed=1
+  done
+  return $failed
+}

updates.d/46-neovim.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+# Only the plugins are updated; the kickstart.nvim config itself is the user's to edit.
+is_installed() {
+  command -v nvim &>/dev/null && [ -d "${XDG_DATA_HOME:-$HOME/.local/share}/nvim/lazy/lazy.nvim" ]
+}
+
+run_update() {
+  echo "Updating Neovim plugins..."
+  nvim --headless "+Lazy! sync" +qa
+}

updates.d/60-pipx.sh

@@ -1,4 +1,18 @@
 #!/bin/bash
 
-echo "Updating pipx applications..."
-pipx upgrade-all
+# pipx venvs are tied to the Python they were built with, so a Python upgrade
+# breaks them in a way `pipx upgrade-all` can't repair. Rebuild them when the
+# Python version changes, or when an upgrade fails.
+STAMP="$HOME/.local/state/coredesktop/pipx-python-version"
+CURRENT_PYTHON="$(python3 -c 'import sys; print("%d.%d" % sys.version_info[:2])')"
+
+if [ "$(cat "$STAMP" 2>/dev/null)" != "$CURRENT_PYTHON" ]; then
+    echo "Python changed to $CURRENT_PYTHON, reinstalling pipx applications..."
+    pipx reinstall-all
+else
+    echo "Updating pipx applications..."
+    if ! pipx upgrade-all; then
+        echo "pipx upgrade-all failed, reinstalling pipx applications..."
+        pipx reinstall-all
+    fi
+fi && mkdir -p "$(dirname "$STAMP")" && echo "$CURRENT_PYTHON" > "$STAMP"

updates.d/65-migrate.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+is_installed() {
+  [ -f "$HOME/.local/bin/migrate" ]
+}
+
+run_update() {
+  echo "Updating Migrate..."
+  local tmp
+  tmp="$(mktemp)"
+  if curl -fsSL -o "$tmp" https://github.com/CyphrRiot/Migrate/raw/main/bin/migrate && [ -s "$tmp" ]; then
+    chmod +x "$tmp"
+    mv "$tmp" "$HOME/.local/bin/migrate"
+  else
+    rm -f "$tmp"
+    echo "Could not download Migrate; keeping the current version."
+    return 1
+  fi
+}

updates.d/80-gnome-extensions.sh

@@ -0,0 +1,25 @@
+#!/bin/bash
+
+is_installed() {
+  command -v gnome-shell &>/dev/null
+}
+
+run_update() {
+  echo "Updating GNOME extensions..."
+
+  # Reinstall gext if missing or broken (e.g. its pipx venv went stale after a Python upgrade)
+  if ! ~/.local/bin/gext --version &> /dev/null; then
+    echo "gext missing or broken, reinstalling..."
+    pipx uninstall gnome-extensions-cli 2>/dev/null || true
+    pipx install --python "$(which python3)" gnome-extensions-cli --system-site-packages
+  fi
+
+  # Update every enabled user extension to the latest version for this GNOME Shell.
+  # The filesystem backend writes directly to ~/.local/share/gnome-shell/extensions;
+  # GNOME Shell picks up the new code at next login.
+  if ~/.local/bin/gext --filesystem update --user --yes; then
+    echo "GNOME extensions up to date. Log out and back in to load any updated extensions."
+  else
+    echo "gext update failed; GNOME extensions were not updated."
+  fi
+}

updates.d/85-gnome-settings.sh

@@ -0,0 +1,11 @@
+#!/bin/bash
+
+COREDESKTOP="$HOME/.local/share/coredesktop"
+
+is_installed() {
+  command -v dconf &>/dev/null
+}
+
+run_update() {
+  bash "$COREDESKTOP/gnome/apply-gnome-settings.sh"
+}

updates.d/90-firmware.sh

@@ -0,0 +1,18 @@
+#!/bin/bash
+
+# Firmware updates often need a reboot, so this only reports what's available.
+is_installed() {
+  command -v fwupdmgr &>/dev/null
+}
+
+run_update() {
+  echo "Checking for firmware updates..."
+  fwupdmgr refresh &>/dev/null
+  # get-updates exits 2 when there is nothing to update
+  if fwupdmgr get-updates --no-unreported-check 2>/dev/null; then
+    echo "Firmware updates are available. Run 'fwupdmgr update' to install them."
+  else
+    echo "No firmware updates available."
+  fi
+  return 0
+}

updates.d/95-cleanup.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+
+echo "Removing unused Flatpak runtimes..."
+flatpak uninstall --unused -y --noninteractive
+
+if command -v paccache &>/dev/null; then
+  echo "Trimming pacman package cache..."
+  sudo paccache -rk2
+  sudo paccache -ruk0
+fi

updates.d/99-reboot-check.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+# If the running kernel's modules are gone, a newer kernel was installed
+if [ ! -d "/usr/lib/modules/$(uname -r)" ]; then
+  echo "A newer kernel has been installed. Please reboot when convenient."
+fi

utils.sh

@@ -60,3 +60,15 @@ remove_flatpaks() {
     flatpak uninstall --noninteractive "${to_remove[@]}"
   fi
 }
+
+# Function to enable systemd services if not already enabled
+enable_services() {
+  for service in "$@"; do
+    if ! systemctl is-enabled "$service" &> /dev/null; then
+      echo "Enabling $service..."
+      sudo systemctl enable "$service"
+    else
+      echo "$service is already enabled."
+    fi
+  done
+}