**System details:** Omarchy quattro upgrade via `omarchy-upgrade-to-quattro`, Hyprland session.

## What happened

After running `omarchy upgrade to quattro`, all bar customizations and enabled plugins disappeared: extra bar widgets (a third-party plugin widget, media, a theme switcher, active-window, others), the enabled-plugins list, `transparent: true`, and custom idle timers were all gone, reset to stock quattro defaults. Nothing was actually deleted from disk — every plugin directory under `~/.config/omarchy/plugins/` was untouched — only `~/.config/omarchy/shell.json` had been reset.

## Root cause

`omarchy-upgrade-to-quattro` lists `omarchy/shell.json` in `always_copy_config_files` (around line 1641), with the comment:

```
# These new Omarchy quattro config entry points. Older installs cannot have
# Omarchy-shipped legacy copy hash-match, so always install quattro default.
```

`backup_config_file()` does save the previous file to `shell.json.omarchy-upgrade-to-quattro.<timestamp>.bak` before overwriting, so the data isn't lost — but the live file is unconditionally replaced with the stock quattro default regardless of whether the user's existing `shell.json` was already valid, parseable, and customized. There's no attempt to merge the user's `bar.layout`, `plugins`, `idle`, or `bar.transparent` values onto the new default, and no prompt or notification telling the user this happened or that a `.bak` exists to restore from.

The schema is unchanged between pre- and post-quattro `shell.json` (`bar`, `idle`, `plugins`, `version` — no new required keys), so a straight restore of the `.bak` works fine, which suggests a merge (or even just a "restore any preserved fields the new schema still supports") is feasible instead of a blanket overwrite.

This is the same failure family as #7100 (shell.json getting silently reset to defaults with no data-loss protection) and the same blanket-overwrite pattern flagged in #8173 for a different upgrade-time file, but this is specifically about the quattro upgrade path clobbering a previously valid, user-customized `shell.json`.

## Suggested enhancement

- During the quattro upgrade, migrate/merge the existing `shell.json` (bar layout, plugin list, idle timers, transparency) onto the new default schema instead of unconditionally overwriting it, since the schema is compatible.
- If a full merge isn't feasible for some fields, at minimum print a clear message pointing at the `.bak` file so users know their config was preserved and how to restore it, rather than discovering the loss silently.

## Repro

1. Have a customized `~/.config/omarchy/shell.json` (extra bar widgets, enabled plugins, `transparent: true`, custom idle timers) on a pre-quattro install.
2. Run `omarchy upgrade to quattro`.
3. Observe `~/.config/omarchy/shell.json` now matches the stock quattro default, while `~/.config/omarchy/shell.json.omarchy-upgrade-to-quattro.<timestamp>.bak` contains the pre-upgrade customized config — confirming nothing was lost, just discarded from the live file.