I thought this would work

Author: StanleyGoldman

src/UnityExtension/Assets/Editor/GitHub.Unity/ApplicationCache.cs

@@ -197,7 +197,7 @@ public LocalConfigBranchDictionary(IDictionary<string, ConfigBranch> dictionary)
     }
 
     [Serializable]
-    class RemoteConfigBranchDictionary : SerializableDictionary<string, SerializableDictionary<string, ConfigBranch>>, IRemoteConfigBranchDictionary
+    class RemoteConfigBranchDictionary : SerializableNestedDictionary<string, ConfigBranch>, IRemoteConfigBranchDictionary
     {
         public RemoteConfigBranchDictionary()
         { }
@@ -206,7 +206,7 @@ public RemoteConfigBranchDictionary(IDictionary<string, IDictionary<string, Conf
         {
             foreach (var pair in dictionary)
             {
-                this.Add(pair.Key, new LocalConfigBranchDictionary(pair.Value));
+                Add(pair.Key, pair.Value.ToDictionary(valuePair => valuePair.Key, valuePair => valuePair.Value));
             }
         }
 
@@ -262,7 +262,7 @@ bool IDictionary<string, IDictionary<string, ConfigBranch>>.TryGetValue(string k
         {
             value = null;
 
-            SerializableDictionary<string, ConfigBranch> branches;
+            Dictionary<string, ConfigBranch> branches;
             if (TryGetValue(key, out branches))
             {
                 value = branches;
@@ -610,13 +610,21 @@ public void RemoveRemoteBranch(string remote, string branch)
 
         public void SetRemotes(IDictionary<string, ConfigRemote> remoteDictionary, IDictionary<string, IDictionary<string, ConfigBranch>> branchDictionary)
         {
+            var now = DateTimeOffset.Now;
             configRemotes = new ConfigRemoteDictionary(remoteDictionary);
             remoteConfigBranches = new RemoteConfigBranchDictionary(branchDictionary);
+            Logger.Trace("SetRemotes {0}", now);
+            Logger.Trace("remoteDictionary.Length: {0}", remoteDictionary.Count);
+            Logger.Trace("branchDictionary.Length: {0}", branchDictionary.Count);
+            SaveData(now, true);
         }
 
         public void SetLocals(IDictionary<string, ConfigBranch> branchDictionary)
         {
+            var now = DateTimeOffset.Now;
             localConfigBranches = new LocalConfigBranchDictionary(branchDictionary);
+            Logger.Trace("SetRemotes {0}", now);
+            SaveData(now, true);
         }
 
         public override string LastUpdatedAtString

src/UnityExtension/Assets/Editor/GitHub.Unity/SerializableDictionary.cs

@@ -40,4 +40,56 @@ public void OnAfterDeserialize()
                 this.Add(keys[i], values[i]);
         }
     }
+
+    [Serializable]
+    public class ArrayContainer<T>
+    {
+        [SerializeField]
+        public T[] Values = new T[0];
+    }
+
+    [Serializable]
+    public class SerializableNestedDictionary<TKey, TValue> : Dictionary<TKey, Dictionary<TKey, TValue>>, ISerializationCallbackReceiver
+    {
+        [SerializeField] private TKey[] keys = new TKey[0];
+        [SerializeField] private ArrayContainer<TKey>[] subKeys = new ArrayContainer<TKey>[0];
+        [SerializeField] private ArrayContainer<TValue>[] subKeyValues = new ArrayContainer<TValue>[0];
+
+        // save the dictionary to lists
+        public void OnBeforeSerialize()
+        {
+            var keyList = new List<TKey>();
+            var subKeysList = new List<ArrayContainer<TKey>>();
+            var subKeysValuesList = new List<ArrayContainer<TValue>>();
+
+            foreach (var pair in this)
+            {
+                var pairKey = pair.Key;
+                keyList.Add(pairKey);
+
+                var serializeSubKeys = new List<TKey>();
+                var serializeSubKeyValues = new List<TValue>();
+
+                var subDictionary = pair.Value;
+                foreach (var subPair in subDictionary)
+                {
+                    serializeSubKeys.Add(subPair.Key);
+                    serializeSubKeyValues.Add(subPair.Value);
+                }
+
+                subKeysList.Add(new ArrayContainer<TKey> { Values = serializeSubKeys.ToArray() });
+                subKeysValuesList.Add(new ArrayContainer<TValue> { Values = serializeSubKeyValues.ToArray() });
+            }
+
+            keys = keyList.ToArray();
+            subKeys = subKeysList.ToArray();
+            subKeyValues = subKeysValuesList.ToArray();
+        }
+
+        // load dictionary from lists
+        public void OnAfterDeserialize()
+        {
+            this.Clear();
+        }
+    }
 }