diff --git a/api/src/main/java/com/google/appengine/api/datastore/QueryRunnerV3.java b/api/src/main/java/com/google/appengine/api/datastore/QueryRunnerV3.java
index 02d59ec15..e415844bf 100644
--- a/api/src/main/java/com/google/appengine/api/datastore/QueryRunnerV3.java
+++ b/api/src/main/java/com/google/appengine/api/datastore/QueryRunnerV3.java
@@ -50,7 +50,7 @@ public QueryResultsSource runQuery(FetchOptions fetchOptions, Query query, Trans
 
     Future<DatastoreV3Pb.QueryResult> result =
         DatastoreApiHelper.makeAsyncCall(
-            apiConfig, Method.RunQuery, queryProto.build(), DatastoreV3Pb.QueryResult.newBuilder().build());
+            apiConfig, Method.RunQuery, queryProto.build(), DatastoreV3Pb.QueryResult.newBuilder().buildPartial());
 
     // Adding more info to DatastoreNeedIndexException if thrown
     result =
diff --git a/api_dev/src/main/java/com/google/appengine/api/datastore/dev/PseudoKinds.java b/api_dev/src/main/java/com/google/appengine/api/datastore/dev/PseudoKinds.java
index d43d17183..e2db9cac1 100644
--- a/api_dev/src/main/java/com/google/appengine/api/datastore/dev/PseudoKinds.java
+++ b/api_dev/src/main/java/com/google/appengine/api/datastore/dev/PseudoKinds.java
@@ -38,7 +38,7 @@
  */
 class PseudoKinds {
   // Marker to indicate get() was not called on a pseudo-kind
-  static final EntityProto NOT_A_PSEUDO_KIND = EntityProto.newBuilder().build();
+  static final EntityProto NOT_A_PSEUDO_KIND = EntityProto.newBuilder().buildPartial();
 
   // Key is kind name
   private final Map<String, PseudoKind> pseudoKinds;
diff --git a/appengine-api-1.0-sdk/pom.xml b/appengine-api-1.0-sdk/pom.xml
index 203a8408f..46b24a4a0 100644
--- a/appengine-api-1.0-sdk/pom.xml
+++ b/appengine-api-1.0-sdk/pom.xml
@@ -366,40 +366,10 @@
                 <filter>
                   <artifact>com.google.appengine:protos</artifact>
                   <includes>
-                    <include>com/google/appengine/api/**</include>
-                    <include>com/google/apphosting/api/**</include>
-                    <include>com/google/apphosting/datastore/proto2api/**</include>
-                    <include>com/google/apphosting/base/protos/Codes*</include>
-                    <include>com/google/apphosting/base/protos/SourcePb*</include>
-                    <include>com/google/apphosting/base/protos/api/ApiBasePb*</include>
-                    <include>com/google/apphosting/base/protos/api/RemoteApiPb*</include>
-                    <include>com/google/protos/proto2/bridge/*</include>
-                    <include>com/google/storage/onestore/v3/proto2api/*</include>
-                    <include>com/google/apphosting/executor/*</include>
-                  </includes>
-                </filter>
-                <filter>
-                  <artifact>com.google.appengine:proto1</artifact>
-                  <includes>
-                    <include>com/google/appengine/api/taskqueue/*</include>
-                    <include>com/google/apphosting/datastore/**</include>
-                    <include>com/google/apphosting/utils/remoteapi/*</include>
-                    <include>com/google/common/annotations/GoogleInternal*</include>
-                    <include>com/google/common/base/StringUtil*</include>
-                    <include>com/google/common/util/concurrent/internal/*</include>
-                    <include>com/google/common/flags/*</include>
-                    <include>com/google/common/flags/ext/*</include>
-                    <include>com/google/io/base/**</include>
-                    <include>com/google/io/protocol/**</include>
-                    <include>com/google/protobuf/**</include>
-                    <include>com/google/storage/onestore/v3/OnestoreAction*</include>
-                    <include>com/google/storage/onestore/v3/OnestoreEntity*</include>
-                    <include>com/google/storage/onestore/v3/OnestoreSnapshot*</include>
-                    <include>com/google/storage/onestore/v3/proto2api/OnestoreAction*</include>
-                    <include>com/google/storage/onestore/v3/proto2api/OnestoreEntity*</include>
-                    <include>com/google/storage/onestore/v3/proto2api/OnestoreSnapshot*</include>
+                    <include>com/**</include>
                   </includes>
                 </filter>
+
                 <filter>
                   <artifact>com.google.appengine:runtime-shared</artifact>
                   <excludes>
@@ -487,7 +457,6 @@
                   <include>com.google.appengine:appengine-apis:*</include>
                   <include>com.google.appengine:appengine-utils:*</include>
                   <include>com.google.appengine:geronimo-javamail_1.4_spec:*</include>
-                  <include>com.google.appengine:proto1:*</include>
                   <include>com.google.appengine:protos:*</include>
                   <include>com.google.appengine:runtime-shared:*</include>
                   <include>com.google.cloud.datastore:datastore-v1-proto-client:*</include>
diff --git a/lib/tools_api/pom.xml b/lib/tools_api/pom.xml
index 04224f713..9286bad64 100644
--- a/lib/tools_api/pom.xml
+++ b/lib/tools_api/pom.xml
@@ -193,16 +193,7 @@
                     <include>com/google/appengine/tools/util/**</include>
                   </includes>
                 </filter>
-                <filter>
-                  <artifact>com.google.appengine:proto1:*</artifact>
-                  <includes>
-                    <include>com/google/common/annotations/GoogleInternal*</include>
-                    <include>com/google/common/base/StringUtil*</include>
-                    <include>com/google/common/util/concurrent/internal/*</include>
-                    <include>com/google/common/flags/*</include>
-                    <include>com/google/protobuf/**</include>
-                  </includes>
-                </filter>
+
                 <filter>
                   <artifact>com.google.protobuf:protobuf-java</artifact>
                   <includes>
@@ -294,7 +285,6 @@
                   <include>com.google.appengine:appengine-apis-dev</include>
                   <include>com.google.appengine:shared-sdk</include>
                   <include>com.google.appengine:protos</include>
-                  <include>com.google.appengine:proto1:*</include>
                   <include>com.google.appengine:appengine-utils</include>
                   <include>com.google.flogger:google-extensions</include>
                   <include>com.google.flogger:flogger-system-backend</include>
diff --git a/lib/tools_api/src/main/java/com/google/appengine/tools/JarSplitterMain.java b/lib/tools_api/src/main/java/com/google/appengine/tools/JarSplitterMain.java
deleted file mode 100644
index e38c49651..000000000
--- a/lib/tools_api/src/main/java/com/google/appengine/tools/JarSplitterMain.java
+++ /dev/null
@@ -1,99 +0,0 @@
-/*
- * Copyright 2021 Google LLC
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *     https://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
-
-package com.google.appengine.tools;
-
-import com.google.appengine.tools.util.JarSplitter;
-import com.google.common.flags.Flag;
-import com.google.common.flags.FlagSpec;
-import com.google.common.flags.Flags;
-import java.io.File;
-import java.io.IOException;
-import java.util.Set;
-
-/**
- * Simple utility that splits a large jar file into one or more jar
- * files that are each less than the file size specified with
- * --max_file_size.
- *
- * This class strips out jar index files.  It does not, however,
- * ensure that resource or META-INF files are directed to the
- * appropriate jar file.  It's unclear whether this will cause
- * problems or not.
- *
- * UPDATE to the lack of clarity:  It is now clear that this will
- * cause problems.  Some frameworks (datanucleus in particular)
- * make assumptions about the colocation of well-known files
- * and the manifest in the same jar.  Splitting the jar
- * violates these assumptions.
- *
- * Usage:
- * <pre>
- *   JarSplitter --input_jar=MyProject_deploy.jar \
- *               --output_directory=./lib \
- *               --max_file_size=10000000 \
- *               --replicate_manifests=false \
- *               --exclude_suffixes=.so,.dll
- *
- */
-public class JarSplitterMain {
-  @FlagSpec(
-      help = "The maximum file for each output jar file.",
-      name = "max_file_size",
-      altName = "MAX_FILE_SIZE")
-  public static final Flag<Integer> MAX_FILE_SIZE = Flag.value(10 * 1024 * 1024);
-
-  @FlagSpec(help = "The input jar file.", name = "input_jar", altName = "INPUT_JAR")
-  public static final Flag<String> INPUT_JAR = Flag.value("input.jar");
-
-  @FlagSpec(
-      help = "The directory where output jars will be written.",
-      name = "output_directory",
-      altName = "OUTPUT_DIRECTORY")
-  public static final Flag<String> OUTPUT_DIRECTORY = Flag.value(".");
-
-  @FlagSpec(
-      help = "The number of digits used for the output files.",
-      name = "output_digits",
-      altName = "OUTPUT_DIGITS")
-  public static final Flag<Integer> OUTPUT_DIGITS = Flag.value(4);
-
-  @FlagSpec(
-      help =
-          "Whether or not manifests are replicated across all split jars.  If false, manifests are"
-              + " ignored.",
-      name = "replicate_manifests",
-      altName = "REPLICATE_MANIFESTS")
-  public static final Flag<Boolean> REPLICATE_MANIFESTS = Flag.value(Boolean.FALSE);
-
-  @FlagSpec(
-      help = "A set of filename suffixes that will be excluded from all jars",
-      name = "exclude_suffixes",
-      altName = "EXCLUDE_SUFFIXES")
-  public static final Flag<Set<String>> EXCLUDE_SUFFIXES = Flag.stringSet();
-
-  public static void main(String[] args) throws IOException {
-    args = Flags.parseAndReturnLeftovers(args);
-
-    JarSplitter splitter = new JarSplitter(new File(INPUT_JAR.get()),
-                                           new File(OUTPUT_DIRECTORY.get()),
-                                           MAX_FILE_SIZE.get(),
-                                           REPLICATE_MANIFESTS.get(),
-                                           OUTPUT_DIGITS.get(),
-                                           EXCLUDE_SUFFIXES.get());
-    splitter.run();
-  }
-}
diff --git a/pom.xml b/pom.xml
index 6de46b092..e7d0ba1bd 100644
--- a/pom.xml
+++ b/pom.xml
@@ -347,15 +347,10 @@
         <artifactId>httpcore-nio</artifactId>
         <version>4.4.16</version>
       </dependency>
-      <dependency>
-        <groupId>com.google.appengine</groupId>
-        <artifactId>proto1</artifactId>
-        <version>0.7</version>
-      </dependency>
       <dependency>
         <groupId>com.google.cloud.datastore</groupId>
         <artifactId>datastore-v1-proto-client</artifactId>
-        <version>2.18.2</version> <!--keep>-->
+        <version>2.22.0</version>
       </dependency>
       <dependency>
         <groupId>com.google.geometry</groupId>
@@ -418,12 +413,12 @@
       <dependency>
         <groupId>com.google.api.grpc</groupId>
         <artifactId>proto-google-cloud-datastore-v1</artifactId>
-        <version>0.108.5</version>  <!--keep--> 
+        <version>0.112.1</version> 
       </dependency>
       <dependency>
         <groupId>com.google.api.grpc</groupId>
         <artifactId>proto-google-common-protos</artifactId>
-        <version>2.32.0</version> <!--keep-->
+        <version>2.46.0</version> 
       </dependency>
       <dependency>
         <groupId>com.google.code.findbugs</groupId>
@@ -475,12 +470,12 @@
       <dependency>
         <groupId>com.google.protobuf</groupId>
         <artifactId>protobuf-java</artifactId>
-        <version>3.25.1</version> <!-- keep -->
+        <version>3.25.5</version>
       </dependency>
       <dependency>
         <groupId>com.google.protobuf</groupId>
         <artifactId>protobuf-java-util</artifactId>
-        <version>3.25.1</version> <!-- keep -->
+        <version>3.25.5</version>
       </dependency>
       <dependency>
         <groupId>javax.activation</groupId>
@@ -851,7 +846,7 @@
                  https://github.com/protocolbuffers/protobuf/blob/master/java/pom.xml#L7
                  Read https://github.com/os72/protoc-jar-maven-plugin/issues/107 for context.
              -->
-             <protocVersion>3.25.1</protocVersion>
+             <protocVersion>3.25.5</protocVersion>
           </configuration>
         </plugin>
         <plugin>
diff --git a/runtime/impl/pom.xml b/runtime/impl/pom.xml
index 600365f6b..d021dba40 100644
--- a/runtime/impl/pom.xml
+++ b/runtime/impl/pom.xml
@@ -222,11 +222,6 @@
             <artifactId>appengine-tools-sdk</artifactId>
             <scope>test</scope>
         </dependency>
-        <dependency>
-            <groupId>com.google.appengine</groupId>
-            <artifactId>proto1</artifactId>
-            <optional>true</optional>
-        </dependency>
         <dependency>
            <groupId>javax.activation</groupId>
            <artifactId>activation</artifactId>
diff --git a/runtime/local_jetty12/pom.xml b/runtime/local_jetty12/pom.xml
index 6de32af57..66cb61343 100644
--- a/runtime/local_jetty12/pom.xml
+++ b/runtime/local_jetty12/pom.xml
@@ -73,10 +73,6 @@
       <groupId>com.google.protobuf</groupId>
       <artifactId>protobuf-java</artifactId>
    </dependency>
-    <dependency>
-      <groupId>com.google.appengine</groupId>
-      <artifactId>proto1</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.eclipse.jetty.ee8</groupId>
       <artifactId>jetty-ee8-webapp</artifactId>
@@ -251,18 +247,6 @@
                     <include>com/google/appengine/tools/development/proto/**</include>
                   </includes>
                 </filter>
-                <filter>
-                  <artifact>com.google.appengine:proto1:*</artifact>
-                  <includes>
-                    <include>com/google/common/flags/*</include>
-                    <include>com/google/common/flags/ext/*</include>
-                    <include>com/google/io/protocol/**</include>
-                    <include>com/google/protobuf/**</include>
-                  </includes>
-                  <excludes>
-                    <exclude>com/google/io/protocol/proto2/*</exclude>
-                  </excludes>
-                </filter>
                 <filter>
                   <artifact>com.google.appengine:shared-sdk-jetty12:*</artifact>
                   <includes>
diff --git a/runtime/local_jetty12_ee10/pom.xml b/runtime/local_jetty12_ee10/pom.xml
index 49be12bd6..09c8ddbaa 100644
--- a/runtime/local_jetty12_ee10/pom.xml
+++ b/runtime/local_jetty12_ee10/pom.xml
@@ -73,10 +73,6 @@
       <groupId>com.google.protobuf</groupId>
       <artifactId>protobuf-java</artifactId>
    </dependency>
-    <dependency>
-      <groupId>com.google.appengine</groupId>
-      <artifactId>proto1</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.eclipse.jetty.ee10</groupId>
       <artifactId>jetty-ee10-webapp</artifactId>
diff --git a/runtime/local_jetty9/pom.xml b/runtime/local_jetty9/pom.xml
index f309bea1b..4d0777033 100644
--- a/runtime/local_jetty9/pom.xml
+++ b/runtime/local_jetty9/pom.xml
@@ -68,10 +68,6 @@
       <groupId>com.google.protobuf</groupId>
       <artifactId>protobuf-java</artifactId>
    </dependency>
-    <dependency>
-      <groupId>com.google.appengine</groupId>
-      <artifactId>proto1</artifactId>
-    </dependency>
     <dependency>
       <groupId>org.eclipse.jetty</groupId>
       <artifactId>jetty-webapp</artifactId>
@@ -187,18 +183,6 @@
                     <include>com/google/appengine/tools/development/proto/**</include>
                   </includes>
                 </filter>
-                <filter>
-                  <artifact>com.google.appengine:proto1:*</artifact>
-                  <includes>
-                    <include>com/google/common/flags/*</include>
-                    <include>com/google/common/flags/ext/*</include>
-                    <include>com/google/io/protocol/**</include>
-                    <include>com/google/protobuf/**</include>
-                  </includes>
-                  <excludes>
-                    <exclude>com/google/io/protocol/proto2/*</exclude>
-                  </excludes>
-                </filter>
                 <filter>
                   <artifact>com.google.appengine:shared-sdk-jetty9:*</artifact>
                   <includes>
diff --git a/runtime/runtime_impl_jetty12/pom.xml b/runtime/runtime_impl_jetty12/pom.xml
index 000f1927d..10ca56c32 100644
--- a/runtime/runtime_impl_jetty12/pom.xml
+++ b/runtime/runtime_impl_jetty12/pom.xml
@@ -287,11 +287,6 @@
       <!-- Test dependencies. -->
 
 
-        <dependency>
-            <groupId>com.google.appengine</groupId>
-            <artifactId>proto1</artifactId>
-            <optional>true</optional>
-        </dependency>
         <dependency>
            <groupId>javax.activation</groupId>
            <artifactId>activation</artifactId>
@@ -401,28 +396,7 @@
                                 <filter>
                                     <artifact>com.google.appengine:protos</artifact>
                                     <includes>
-                                        <include>com/google/apphosting/api/**</include>
-                                        <include>com/google/apphosting/base/protos/*</include>
-                                        <include>com/google/apphosting/base/protos/api/*</include>
-                                        <include>com/google/apphosting/datastore/proto2api/**</include>
-                                        <include>com/google/cloud/datastore/logs/*</include>
-                                        <include>com/google/storage/onestore/v3/proto2api/*</include>
-                                        <include>com/google/appengine/api/appidentity/*</include>
-                                        <include>com/google/appengine/api/datastore/*</include>
-                                        <include>com/google/appengine/api/memcache/*</include>
-                                        <include>com/google/appengine/api/oauth/*</include>
-                                        <include>com/google/appengine/api/taskqueue/*</include>
-                                        <include>com/google/appengine/api/urlfetch/*</include>
-                                        <include>com/google/appengine/api/users/*</include>
-                                        <include>com/google/appengine/api/utils/*</include>
-                                        <include>com/google/apphosting/datastore/proto2api/**</include>
-                                        <include>com/google/apphosting/base/protos/Codes*</include>
-                                        <include>com/google/apphosting/base/protos/SourcePb*</include>
-                                        <include>com/google/apphosting/base/protos/api/ApiBasePb*</include>
-                                        <include>com/google/apphosting/base/protos/api/RemoteApiPb*</include>
-                                        <include>com/google/protos/proto2/bridge/*</include>
-                                        <include>com/google/storage/onestore/v3/proto2api/*</include>
-                                        <include>com/google/apphosting/executor/*</include>
+                                        <include>com/**</include>
                                   </includes>
                                 </filter>
                                   <filter>
@@ -501,7 +475,6 @@
                                     <include>com.google.api.grpc:proto-google-common-protos</include>
                                     <include>com.google.appengine:appengine-utils</include>
                                     <include>com.google.appengine:runtime-impl</include>
-                                    <include>com.google.appengine:proto1</include>
                                     <include>com.google.appengine:protos</include>
                                     <include>com.google.appengine:runtime-util</include>
                                     <include>com.google.appengine:appengine-apis</include>
diff --git a/runtime/runtime_impl_jetty9/pom.xml b/runtime/runtime_impl_jetty9/pom.xml
index 87d03f2b6..4d7c95c49 100644
--- a/runtime/runtime_impl_jetty9/pom.xml
+++ b/runtime/runtime_impl_jetty9/pom.xml
@@ -253,11 +253,6 @@
             <optional>true</optional>
         </dependency>
         <!-- Test dependencies. -->
-        <dependency>
-            <groupId>com.google.appengine</groupId>
-            <artifactId>proto1</artifactId>
-            <optional>true</optional>
-        </dependency>
         <dependency>
            <groupId>javax.activation</groupId>
            <artifactId>activation</artifactId>
@@ -406,7 +401,6 @@
                                     <include>com.google.api.grpc:proto-google-common-protos</include>
                                     <include>com.google.appengine:appengine-utils</include>
                                     <include>com.google.appengine:runtime-impl</include>
-                                    <include>com.google.appengine:proto1</include>
                                     <include>com.google.appengine:protos</include>
                                     <include>com.google.appengine:runtime-util</include>
                                     <include>com.google.appengine:appengine-apis</include>