core: get rid of noteIds in notebook topics

This is a BREAKING change in the core & will require updating the
clients. The way it works is instead of keeping noteIds of all the
notes in the topic, it keeps an in-memory cache. This in-memory
cache `topicReferences` lives in the notes collection & decouples
notes from notebooks/topics. This also simplifies all the different
actions where references would persist after the note was deleted.
Since the note acts as the source of truth for where it currently is,
there is nothing else to do except rebuild the `topicReferences`
cache.

packages/core/api/sync/index.js

@@ -371,6 +371,8 @@ class Sync {
   async onRemoteSyncCompleted(lastSynced) {
     // refresh monographs on sync completed
     await this.db.monographs.init();
+    // refresh topic references
+    this.db.notes.topicReferences.refresh();
 
     await this.start(false, false, lastSynced);
   }