Unstick plugins lazy.nvim won't update, and move to Thunderbird ESR

An interrupted plugin update can leave a plugin's files out of step with
its checkout, and lazy.nvim then refuses to update it, every time. Before
syncing, update now stashes such changes, so they can still be recovered
with git stash pop, and puts the plugin's submodules back.

Flathub retired org.mozilla.Thunderbird in favor of
org.mozilla.thunderbird_esr, so update tried to reinstall the old ID on
every run. Install the new one. flatpak update already moves existing
installs over; a migration carries a skip-packages entry for the old ID
over to the new one.

Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>

updates.d/46-neovim.sh

@@ -1,11 +1,29 @@
 #!/bin/bash
 
 # Only the plugins are updated; the kickstart.nvim config itself is the user's to edit.
+LAZY_DIR="${XDG_DATA_HOME:-$HOME/.local/share}/nvim/lazy"
+
 is_installed() {
-  command -v nvim &>/dev/null && [ -d "${XDG_DATA_HOME:-$HOME/.local/share}/nvim/lazy/lazy.nvim" ]
+  command -v nvim &>/dev/null && [ -d "$LAZY_DIR/lazy.nvim" ]
+}
+
+# lazy.nvim won't update a plugin whose tracked files differ from its checkout
+# (it checks with `git ls-files -d -m`), which an interrupted update can leave
+# behind. Stash those changes, so the plugin updates and they can still be
+# recovered with `git stash pop` in its folder, and put its submodules back.
+restore_plugins() {
+  local dir
+  for dir in "$LAZY_DIR"/*/; do
+    [ -d "$dir/.git" ] || continue
+    [ -n "$(git -C "$dir" ls-files -d -m 2> /dev/null)" ] || continue
+    echo "  $(basename "$dir") had local changes; stashing them so it can update."
+    git -C "$dir" stash push -q -m "Stashed by CoreDesktop's update" \
+      && git -C "$dir" submodule update -q --init --recursive --force
+  done
 }
 
 run_update() {
   echo "Updating Neovim plugins..."
+  restore_plugins
   nvim --headless "+Lazy! sync" +qa
 }