fix(notifications/threads): Wave-1 audit fixes (🔴 + web 🟠)

- T1 (🔴): markThreadAsRead no longer receipts the thread ROOT (a 2nd instance
  of the read-marker-corruption regression — opening a thread whose root is old
  re-lit the whole room). Extracted to a pure threadReceipt.ts + 5 regression
  tests.
- N1 (🔴): favicon/tab-title unread count now sums only leaf rooms (was double-
  counting every ancestor-space aggregate in roomToUnread).
- N2 (🔴): notifications/sounds dedupe on the event id, not the unread count —
  fixes "read a DM, next message never notifies again".
- T4 (🟠): the thread notification path no longer re-gates on the room count, so
  an explicit per-thread "All replies" override in a Mentions-only room fires.
- N3 (🟠): getUnreadInfos skips phantom {0,0} entries (muted-thread-only rooms no
  longer light the nav row / pollute unread filters).
- N4 (🟠): the Receipt handler recomputes unread instead of blanket-DELETE, so a
  threaded receipt can't wipe a room's valid main-timeline badge.
- T2 (🟠): thread "Jump to Latest" re-anchors the virtual window (was landing on
  a stale mid/old event).

Gates: tsc/eslint/prettier clean, build OK, 678 tests.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>

src/app/state/room/roomToUnread.ts

@@ -24,6 +24,7 @@ import {
   getUnreadInfo,
   getUnreadInfos,
   isNotificationEvent,
+  roomHaveUnread,
 } from '../../utils/room';
 import { roomToParentsAtom } from './roomToParents';
 import { useStateEventCallback } from '../../hooks/useStateEventCallback';
@@ -253,7 +254,20 @@ export const useBindRoomToUnreadAtom = (mx: MatrixClient, unreadAtom: typeof roo
         ),
       );
       if (isMyReceipt) {
-        setUnreadAtom({ type: 'DELETE', roomId: room.roomId });
+        // Don't blanket-DELETE the room's unread on any receipt: a THREADED
+        // receipt (reading one thread) would wipe the room's still-valid
+        // main-timeline badge, and if the room was already read no
+        // UnreadNotifications PUT follows to restore it. Recompute instead —
+        // DELETE only when the room is genuinely fully read.
+        const info = getUnreadInfo(
+          room,
+          getMutedThreads(threadNotificationsRef.current, room.roomId),
+        );
+        if (info.total === 0 && info.highlight === 0 && !roomHaveUnread(mx, room)) {
+          setUnreadAtom({ type: 'DELETE', roomId: room.roomId });
+        } else {
+          setUnreadAtom({ type: 'PUT', unreadInfo: info });
+        }
       }
     };
     mx.on(RoomEvent.Receipt, handleReceipt);