fix: resolve Automerge v3 API compatibility and sync protocol issues

- Fix sync protocol: send full document on client init (required for
  shared history), separate receive from response generation to prevent
  sync state double-advancement
- Strip undefined values from node data before inserting into Automerge
  (Automerge rejects undefined; Node-RED workspaces have undefined props)
- Fix Automerge proxy array issues: use splice() instead of .length=0,
  remove .sort() on proxy arrays (not supported)
- Add stripUndefined utility to both server schema and client module
- All server-side tests pass: 30/30 schema, 16/16 sync protocol
- Editor loads with 0 JS errors, WASM initializes, document loads from
  server successfully

Author: Sprite

packages/node_modules/@node-red/editor-client/src/js/automerge.js

@@ -25,6 +25,18 @@
 RED.automerge = (function() {
     const SCHEMA_VERSION = "1.0";
 
+    function stripUndefined(obj) {
+        if (obj === null || typeof obj !== 'object') return obj;
+        if (Array.isArray(obj)) return obj.map(stripUndefined);
+        var result = {};
+        for (var key in obj) {
+            if (obj.hasOwnProperty(key) && obj[key] !== undefined) {
+                result[key] = stripUndefined(obj[key]);
+            }
+        }
+        return result;
+    }
+
     let Automerge = null;
     let doc = null;
     let syncState = null;
@@ -69,14 +81,14 @@ RED.automerge = (function() {
 
         for (const node of flows) {
             if (node.type === 'tab') {
-                docData.workspaces[node.id] = { ...node };
+                docData.workspaces[node.id] = stripUndefined({ ...node });
                 workspaceOrder.push(node.id);
             } else if (node.type === 'subflow') {
-                docData.subflows[node.id] = { ...node };
+                docData.subflows[node.id] = stripUndefined({ ...node });
             } else if (node.type === 'group') {
-                docData.groups[node.id] = { ...node };
+                docData.groups[node.id] = stripUndefined({ ...node });
             } else {
-                docData.nodes[node.id] = { ...node };
+                docData.nodes[node.id] = stripUndefined({ ...node });
             }
         }
 
@@ -172,9 +184,9 @@ RED.automerge = (function() {
             return;
         }
 
-        // Create initial empty document
-        doc = Automerge.from(createEmptyDoc());
-        syncState = Automerge.initSyncState();
+        // Doc starts null — will be loaded from server's init response
+        doc = null;
+        syncState = null;
 
         // Subscribe to sync messages
         RED.comms.subscribe("automerge/#", handleSyncMessage);
@@ -184,7 +196,7 @@ RED.automerge = (function() {
 
         initialized = true;
 
-        // Request initial state
+        // Request initial state (server will send full document)
         RED.comms.send('automerge/init', {});
     }
 
@@ -210,7 +222,31 @@ RED.automerge = (function() {
     function handleSyncMessage(topic, data) {
         if (!enabled || !Automerge) return;
 
-        if (topic === 'automerge/sync') {
+        if (topic === 'automerge/init') {
+            // Server sent the full document — load it to share history
+            try {
+                const binaryString = atob(data.document);
+                const binary = new Uint8Array(binaryString.length);
+                for (let i = 0; i < binaryString.length; i++) {
+                    binary[i] = binaryString.charCodeAt(i);
+                }
+
+                const oldDoc = doc;
+                doc = Automerge.load(binary);
+                syncState = Automerge.initSyncState();
+
+                console.log("Automerge: Loaded document from server (v" + data.version + ")");
+
+                // Apply any differences to the editor
+                if (oldDoc) {
+                    applyRemoteChanges(oldDoc, doc);
+                }
+            } catch (err) {
+                console.error("Failed to load Automerge document from server:", err);
+            }
+        } else if (topic === 'automerge/sync') {
+            if (!doc || !syncState) return; // Not yet initialized
+
             // Decode base64 message
             let syncMessage;
             try {
@@ -254,8 +290,6 @@ RED.automerge = (function() {
             } catch (err) {
                 console.error("Error processing sync message:", err);
             }
-        } else if (topic === 'automerge/state') {
-            console.log("Automerge state:", data);
         }
     }
 
@@ -472,16 +506,16 @@ RED.automerge = (function() {
             const type = node.type;
 
             if (type === 'tab') {
-                d.workspaces[node.id] = { ...node };
+                d.workspaces[node.id] = stripUndefined({ ...node });
                 if (!d.workspaceOrder.includes(node.id)) {
                     d.workspaceOrder.push(node.id);
                 }
             } else if (type === 'subflow') {
-                d.subflows[node.id] = { ...node };
+                d.subflows[node.id] = stripUndefined({ ...node });
             } else if (type === 'group') {
-                d.groups[node.id] = { ...node };
+                d.groups[node.id] = stripUndefined({ ...node });
             } else {
-                d.nodes[node.id] = { ...node };
+                d.nodes[node.id] = stripUndefined({ ...node });
             }
 
             d.meta.lastModified = Date.now();
@@ -595,7 +629,6 @@ RED.automerge = (function() {
 
             if (!node.wires[sourcePort].includes(targetId)) {
                 node.wires[sourcePort].push(targetId);
-                node.wires[sourcePort].sort();
             }
 
             d.meta.lastModified = Date.now();
@@ -722,7 +755,7 @@ RED.automerge = (function() {
             for (const key of Object.keys(d.groups)) {
                 delete d.groups[key];
             }
-            d.workspaceOrder.length = 0;
+            d.workspaceOrder.splice(0, d.workspaceOrder.length);
 
             // Copy new data
             for (const [key, value] of Object.entries(newDocData.workspaces)) {

packages/node_modules/@node-red/runtime/lib/automerge/index.js

@@ -171,7 +171,7 @@ function setFlows(flows) {
         for (const key of Object.keys(d.groups)) {
             delete d.groups[key];
         }
-        d.workspaceOrder.length = 0;
+        d.workspaceOrder.splice(0, d.workspaceOrder.length);
 
         // Copy new data
         for (const [key, value] of Object.entries(newDoc.workspaces)) {
@@ -205,7 +205,7 @@ function setFlows(flows) {
  * @returns {Uint8Array|null} Response sync message
  */
 function receiveSyncMessage(session, syncMessage) {
-    if (!enabled || !doc) return null;
+    if (!enabled || !doc) return false;
 
     let syncState = syncStates.get(session);
     if (!syncState) {
@@ -223,26 +223,18 @@ function receiveSyncMessage(session, syncMessage) {
         doc = newDoc;
         syncStates.set(session, newSyncState);
 
-        // Generate response message
-        const [nextSyncState, responseMessage] = Automerge.generateSyncMessage(
-            doc,
-            newSyncState
-        );
-
-        if (responseMessage) {
-            syncStates.set(session, nextSyncState);
-        }
+        const changed = oldDoc !== newDoc;
 
         // If the document changed, save and notify other clients
-        if (oldDoc !== newDoc) {
+        if (changed) {
             scheduleSave();
             broadcastSyncExcept(session);
         }
 
-        return responseMessage;
+        return changed;
     } catch (err) {
         runtime.log.warn("Error processing sync message: " + err.message);
-        return null;
+        return false;
     }
 }
 
@@ -283,8 +275,11 @@ function handleSyncMessage(opts) {
         return;
     }
 
-    const response = receiveSyncMessage(session, syncMessage);
+    // Receive the sync message (updates doc and sync state)
+    receiveSyncMessage(session, syncMessage);
 
+    // Generate and send response
+    const response = generateSyncMessage(session);
     if (response) {
         runtime.events.emit('comms', {
             topic: 'automerge/sync',
@@ -301,35 +296,26 @@ function handleSyncMessage(opts) {
  * @param {Object} opts - Message options
  */
 function handleInitRequest(opts) {
-    if (!enabled) return;
+    if (!enabled || !doc) return;
 
     const { session } = opts;
 
-    // Reset sync state for this client
-    syncStates.set(session, Automerge.initSyncState());
+    // Send the full document binary so the client can load it
+    // and share history (required for sync protocol to work)
+    const docBinary = Automerge.save(doc);
 
-    // Generate initial sync message
-    const message = generateSyncMessage(session);
-
-    if (message) {
-        runtime.events.emit('comms', {
-            topic: 'automerge/sync',
-            data: {
-                message: Buffer.from(message).toString('base64')
-            },
-            session: session
-        });
-    }
-
-    // Also send current state info
     runtime.events.emit('comms', {
-        topic: 'automerge/state',
+        topic: 'automerge/init',
         data: {
             enabled: true,
-            version: schema.SCHEMA_VERSION
+            version: schema.SCHEMA_VERSION,
+            document: Buffer.from(docBinary).toString('base64')
         },
         session: session
     });
+
+    // Reset sync state for this client (now they share history)
+    syncStates.set(session, Automerge.initSyncState());
 }
 
 /**

packages/node_modules/@node-red/runtime/lib/automerge/schema.js

@@ -30,6 +30,21 @@
 
 const SCHEMA_VERSION = "1.0";
 
+/**
+ * Strip undefined values from an object (Automerge rejects undefined)
+ */
+function stripUndefined(obj) {
+    if (obj === null || typeof obj !== 'object') return obj;
+    if (Array.isArray(obj)) return obj.map(stripUndefined);
+    const result = {};
+    for (const [key, value] of Object.entries(obj)) {
+        if (value !== undefined) {
+            result[key] = stripUndefined(value);
+        }
+    }
+    return result;
+}
+
 /**
  * Create an empty Automerge document structure
  * @returns {Object} Empty document structure
@@ -65,14 +80,14 @@ function flowsToDoc(flows) {
 
     for (const node of flows) {
         if (node.type === 'tab') {
-            doc.workspaces[node.id] = { ...node };
+            doc.workspaces[node.id] = stripUndefined({ ...node });
             workspaceOrder.push(node.id);
         } else if (node.type === 'subflow') {
-            doc.subflows[node.id] = { ...node };
+            doc.subflows[node.id] = stripUndefined({ ...node });
         } else if (node.type === 'group') {
-            doc.groups[node.id] = { ...node };
+            doc.groups[node.id] = stripUndefined({ ...node });
         } else {
-            doc.nodes[node.id] = { ...node };
+            doc.nodes[node.id] = stripUndefined({ ...node });
         }
     }
 
@@ -171,16 +186,16 @@ function setNode(doc, node) {
     const type = node.type;
 
     if (type === 'tab') {
-        doc.workspaces[node.id] = { ...node };
+        doc.workspaces[node.id] = stripUndefined({ ...node });
         if (!doc.workspaceOrder.includes(node.id)) {
             doc.workspaceOrder.push(node.id);
         }
     } else if (type === 'subflow') {
-        doc.subflows[node.id] = { ...node };
+        doc.subflows[node.id] = stripUndefined({ ...node });
     } else if (type === 'group') {
-        doc.groups[node.id] = { ...node };
+        doc.groups[node.id] = stripUndefined({ ...node });
     } else {
-        doc.nodes[node.id] = { ...node };
+        doc.nodes[node.id] = stripUndefined({ ...node });
     }
 
     doc.meta.lastModified = Date.now();
@@ -286,7 +301,6 @@ function addWire(doc, sourceId, sourcePort, targetId) {
     // Add the target if not already present
     if (!node.wires[sourcePort].includes(targetId)) {
         node.wires[sourcePort].push(targetId);
-        node.wires[sourcePort].sort(); // Maintain sorted order
     }
 
     doc.meta.lastModified = Date.now();
@@ -396,5 +410,6 @@ module.exports = {
     removeWire,
     moveWorkspace,
     addNodeToGroup,
-    removeNodeFromGroup
+    removeNodeFromGroup,
+    stripUndefined
 };