fix(koplugin): honor remote annotation deletions, closes #4119 (#4194)

Pull skipped notes carrying a deleted_at tombstone but never removed the
matching local annotation. A highlight deleted on Readest therefore lingered
in KOReader, and a later push (notably a full sync) re-uploaded it,
resurrecting the note on the server and making it reappear on every device.

Add removeDeletedAnnotations, invoked at the start of the pull callback, to
drop local annotations the server has tombstoned. Tombstones are matched by
stored id, by the hash-derived id for native KOReader highlights, or by
position/page xpointer.

Co-authored-by: Claude Opus 4.7 (1M context) <noreply@anthropic.com>

apps/readest.koplugin/readest_syncannotations.lua

@@ -133,6 +133,75 @@ function SyncAnnotations:getAnnotations(ui, settings, book_hash, meta_hash, full
     return notes
 end
 
+-- Drop local annotations the server has tombstoned (deleted_at set), so a
+-- highlight deleted on Readest also disappears in KOReader. Without this,
+-- pull only skips deleted notes — the local copy lingers and any later
+-- push resurrects it on the server, making it reappear (issue #4119).
+function SyncAnnotations:removeDeletedAnnotations(annotation_mgr, notes, book_hash)
+    local annotations = annotation_mgr and annotation_mgr.annotations
+    if not annotations or #annotations == 0 then return 0 end
+
+    -- Map every local annotation to its index by id and by position so a
+    -- tombstone can be matched however it was originally created: pulled
+    -- notes carry a stored id, native KOReader highlights don't (their id
+    -- is derived from book hash + positions, matching what push uploads).
+    local index_by_id = {}
+    local index_by_anno = {}
+    local index_by_bookmark = {}
+    for i, item in ipairs(annotations) do
+        if item.id then
+            index_by_id[item.id] = i
+        end
+        if item.drawer then
+            local pos0 = item.pos0
+            local pos1 = item.pos1
+            if type(pos0) == "table" then pos0 = nil end
+            if type(pos1) == "table" then pos1 = nil end
+            if pos0 then
+                index_by_anno[tostring(pos0) .. "|" .. tostring(pos1 or "")] = i
+                if not item.id then
+                    local id = self:generateNoteId(book_hash, "annotation", tostring(pos0), pos1 and tostring(pos1))
+                    index_by_id[id] = i
+                end
+            end
+        elseif type(item.page) == "string" then
+            index_by_bookmark[item.page] = i
+            if not item.id then
+                local id = self:generateNoteId(book_hash, "bookmark", item.page)
+                index_by_id[id] = i
+            end
+        end
+    end
+
+    local to_remove = {}
+    for _, note in ipairs(notes) do
+        if note.deleted_at then
+            local idx
+            if note.id and index_by_id[note.id] then
+                idx = index_by_id[note.id]
+            elseif note.type == "bookmark" and note.xpointer0 then
+                idx = index_by_bookmark[note.xpointer0]
+            elseif note.xpointer0 then
+                idx = index_by_anno[note.xpointer0 .. "|" .. (note.xpointer1 or "")]
+            end
+            if idx then
+                to_remove[idx] = true
+            end
+        end
+    end
+
+    -- Remove highest index first so earlier indexes stay valid.
+    local indexes = {}
+    for idx in pairs(to_remove) do
+        indexes[#indexes + 1] = idx
+    end
+    table.sort(indexes, function(a, b) return a > b end)
+    for _, idx in ipairs(indexes) do
+        table.remove(annotations, idx)
+    end
+    return #indexes
+end
+
 function SyncAnnotations:push(ui, settings, client, interactive, full_sync)
     local book_hash = ui.doc_settings:readSetting("partial_md5_checksum")
     local meta_hash = ui.doc_settings:readSetting("readest_sync") or {}
@@ -252,6 +321,10 @@ function SyncAnnotations:pull(ui, settings, client, book_hash, meta_hash, dialog
             local annotation_mgr = ui.annotation
             if not annotation_mgr then return end
 
+            -- Honor remote deletions before adding: drop local annotations
+            -- the server has tombstoned so they don't reappear (issue #4119).
+            local removed = self:removeDeletedAnnotations(annotation_mgr, data, book_hash)
+
             -- Build dedup sets: by ID, by pos0|pos1 for annotations, by page xpointer for bookmarks
             local existing_ids = {}
             local existing_annotations = {}
@@ -378,7 +451,7 @@ function SyncAnnotations:pull(ui, settings, client, book_hash, meta_hash, dialog
                 })
             end
 
-            if added > 0 then
+            if added > 0 or removed > 0 then
                 UIManager:setDirty(dialog, "ui")
             end
         end