Never let a stale settings copy erase a saved choice

The preferences store was loaded once at shell startup, and every save wrote
the whole in-memory copy back. Anything that reached the file after startup --
a hand edit, a script, another shell instance flushing during a session
handoff -- was erased by the next unrelated save. That is how a display scale
set to 1.5 kept coming back as 2: the entry was written, then silently
clobbered, and the catch-all auto rule filled the gap.

Two halves, either alone insufficient. The store now watches its file and
adopts outside writes instead of holding a stale copy over them; and a save
merges with what is on disk rather than overwriting it -- keys this shell has
set win, keys it has never seen survive. A setting changed anywhere now
persists until it is changed again, which is the only behavior a settings
file is entitled to have.

Claude-Session: https://claude.ai/code/session_01Epx9ZC1gwm81K3jm9x9CKh

config/dot/quickshell/config/DesktopPreferences.qml

@@ -130,6 +130,14 @@ Singleton {
         printErrors: false
         atomicWrites: true
 
+        // Adopt writes made from outside the shell -- a hand edit, a script,
+        // a restored snapshot -- instead of holding a stale copy in memory
+        // and silently erasing them at the next save. A change made anywhere
+        // must survive everywhere; the shell is the editor, not the owner.
+        // The shell's own atomic writes land here too and reload as a no-op.
+        watchChanges: true
+        onFileChanged: this.reload()
+
         onLoaded: root.load()
         // No file yet is the normal first-run case, not an error.
         onLoadFailed: root.load()
@@ -145,7 +153,27 @@ Singleton {
     Timer {
         id: persistTimer
         interval: 0
-        onTriggered: preferencesFile.setText(JSON.stringify(root.values, null, 2) + "\n")
+        // Merge with what is on disk rather than overwriting it. This model
+        // was loaded at startup; a key written to the file since then -- a
+        // hand edit, a script, another shell instance during a session
+        // handoff -- would otherwise be erased by the next unrelated save,
+        // which is how a setting "changed itself back". Keys this shell has
+        // set win; keys it has never seen survive.
+        onTriggered: {
+            let disk = {};
+            try {
+                const text = preferencesFile.text();
+                if (text && text.trim().length > 0)
+                    disk = JSON.parse(text);
+            } catch (error) {
+                // An unreadable file loses the merge, never the write.
+            }
+            if (!disk || typeof disk !== "object")
+                disk = {};
+            const merged = Object.assign({}, disk, root.values);
+            root.values = merged;
+            preferencesFile.setText(JSON.stringify(merged, null, 2) + "\n");
+        }
     }
 
     // One-time move from the pre-Stage-1 location inside Quickshell's state