diff --git a/src/main/java/com/google/devtools/build/lib/actions/ActionExecutionContext.java b/src/main/java/com/google/devtools/build/lib/actions/ActionExecutionContext.java
index 4a5e435413f51a..8ee30a9d8fcc7f 100644
--- a/src/main/java/com/google/devtools/build/lib/actions/ActionExecutionContext.java
+++ b/src/main/java/com/google/devtools/build/lib/actions/ActionExecutionContext.java
@@ -98,6 +98,16 @@ public NestedSet<Artifact> getArtifactsAtCanonicalLocationsForLogging() {
     public Map<PathFragment, Artifact> getAllSymlinksForLogging() {
       return wrapped.getAllSymlinksForLogging();
     }
+
+    @Override
+    public NestedSet<String> getEmptyFilenamesForLogging() {
+      return wrapped.getEmptyFilenamesForLogging();
+    }
+
+    @Override
+    public boolean isLegacyExternalRunfiles() {
+      return wrapped.isLegacyExternalRunfiles();
+    }
   }
 
   /**
diff --git a/src/main/java/com/google/devtools/build/lib/actions/RunfilesTree.java b/src/main/java/com/google/devtools/build/lib/actions/RunfilesTree.java
index dbd91a1a0c8920..70a3d5cb41c0b1 100644
--- a/src/main/java/com/google/devtools/build/lib/actions/RunfilesTree.java
+++ b/src/main/java/com/google/devtools/build/lib/actions/RunfilesTree.java
@@ -49,4 +49,8 @@ public interface RunfilesTree {
   NestedSet<Artifact> getArtifactsAtCanonicalLocationsForLogging();
 
   Map<PathFragment, Artifact> getAllSymlinksForLogging();
+
+  NestedSet<String> getEmptyFilenamesForLogging();
+
+  boolean isLegacyExternalRunfiles();
 }
diff --git a/src/main/java/com/google/devtools/build/lib/analysis/Runfiles.java b/src/main/java/com/google/devtools/build/lib/analysis/Runfiles.java
index 6fa1ab50c7e81b..c7ba64e29bae43 100644
--- a/src/main/java/com/google/devtools/build/lib/analysis/Runfiles.java
+++ b/src/main/java/com/google/devtools/build/lib/analysis/Runfiles.java
@@ -251,6 +251,9 @@ public NestedSet<SymlinkEntry> getSymlinks() {
   }
 
   public NestedSet<String> getEmptyFilenames() {
+    if (emptyFilesSupplier == DUMMY_EMPTY_FILES_SUPPLIER) {
+      return NestedSetBuilder.emptySet(Order.STABLE_ORDER);
+    }
     Set<PathFragment> manifestKeys =
         Streams.concat(
                 symlinks.toList().stream().map(SymlinkEntry::getPath),
@@ -399,6 +402,10 @@ public Map<PathFragment, Artifact> getAllSymlinksForLogging(
     return builder.build();
   }
 
+  public boolean isLegacyExternalRunfiles() {
+    return legacyExternalRunfiles;
+  }
+
   /**
    * Helper class to handle munging the paths of external artifacts.
    */
diff --git a/src/main/java/com/google/devtools/build/lib/analysis/RunfilesSupport.java b/src/main/java/com/google/devtools/build/lib/analysis/RunfilesSupport.java
index c1d90d4e44c9bb..678ad9d4744e47 100644
--- a/src/main/java/com/google/devtools/build/lib/analysis/RunfilesSupport.java
+++ b/src/main/java/com/google/devtools/build/lib/analysis/RunfilesSupport.java
@@ -185,6 +185,16 @@ public Map<PathFragment, Artifact> getAllSymlinksForLogging() {
       return runfiles.getAllSymlinksForLogging(repoMappingManifest);
     }
 
+    @Override
+    public NestedSet<String> getEmptyFilenamesForLogging() {
+      return runfiles.getEmptyFilenames();
+    }
+
+    @Override
+    public boolean isLegacyExternalRunfiles() {
+      return runfiles.isLegacyExternalRunfiles();
+    }
+
     @Override
     public RunfileSymlinksMode getSymlinksMode() {
       return runfileSymlinksMode;
diff --git a/src/main/java/com/google/devtools/build/lib/exec/BUILD b/src/main/java/com/google/devtools/build/lib/exec/BUILD
index d9f0be54cebb95..ec4b1f822cd82a 100644
--- a/src/main/java/com/google/devtools/build/lib/exec/BUILD
+++ b/src/main/java/com/google/devtools/build/lib/exec/BUILD
@@ -272,7 +272,7 @@ java_library(
         "SpawnLogContext.java",
     ],
     deps = [
-        ":stable_sort",
+        ":spawn_log_context_utils",
         "//src/main/java/com/google/devtools/build/lib/actions",
         "//src/main/java/com/google/devtools/build/lib/actions:artifacts",
         "//src/main/java/com/google/devtools/build/lib/actions:file_metadata",
@@ -298,13 +298,12 @@ java_library(
 )
 
 java_library(
-    name = "spawn_log_reconstructor",
+    name = "spawn_log_context_utils",
     srcs = [
         "SpawnLogReconstructor.java",
+        "StableSort.java",
     ],
     deps = [
-        ":stable_sort",
-        "//src/main/java/com/google/devtools/build/lib/bazel/rules/python",
         "//src/main/java/com/google/devtools/build/lib/cmdline",
         "//src/main/java/com/google/devtools/build/lib/profiler",
         "//src/main/java/com/google/devtools/build/lib/util:pair",
@@ -317,21 +316,6 @@ java_library(
     ],
 )
 
-java_library(
-    name = "stable_sort",
-    srcs = ["StableSort.java"],
-    deps = [
-        "//src/main/java/com/google/devtools/build/lib/cmdline",
-        "//src/main/java/com/google/devtools/build/lib/profiler",
-        "//src/main/java/com/google/devtools/build/lib/util:pair",
-        "//src/main/java/com/google/devtools/build/lib/util/io:io-proto",
-        "//src/main/java/com/google/devtools/build/lib/vfs:pathfragment",
-        "//src/main/protobuf:spawn_java_proto",
-        "//third_party:guava",
-        "//third_party:jsr305",
-    ],
-)
-
 java_library(
     name = "spawn_runner",
     srcs = [
diff --git a/src/main/java/com/google/devtools/build/lib/exec/CompactSpawnLogContext.java b/src/main/java/com/google/devtools/build/lib/exec/CompactSpawnLogContext.java
index 746e26d3aabe6e..054c62990215e1 100644
--- a/src/main/java/com/google/devtools/build/lib/exec/CompactSpawnLogContext.java
+++ b/src/main/java/com/google/devtools/build/lib/exec/CompactSpawnLogContext.java
@@ -50,6 +50,7 @@
 import com.google.devtools.build.lib.vfs.Symlinks;
 import com.google.devtools.build.lib.vfs.XattrProvider;
 import com.google.errorprone.annotations.CanIgnoreReturnValue;
+import com.google.protobuf.Empty;
 import it.unimi.dsi.fastutil.objects.Object2IntOpenHashMap;
 import java.io.BufferedOutputStream;
 import java.io.IOException;
@@ -60,6 +61,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.SortedMap;
+import java.util.TreeMap;
 import java.util.concurrent.ForkJoinPool;
 import javax.annotation.Nullable;
 import javax.annotation.concurrent.GuardedBy;
@@ -454,7 +456,8 @@ private int logRunfilesTree(
 
           ExecLogEntry.RunfilesTree.Builder builder =
               ExecLogEntry.RunfilesTree.newBuilder()
-                  .setPath(runfilesTree.getExecPath().getPathString());
+                  .setPath(runfilesTree.getExecPath().getPathString())
+                  .setLegacyExternalRunfiles(runfilesTree.isLegacyExternalRunfiles());
 
           builder.setArtifactsId(
               logNestedSet(
@@ -483,6 +486,24 @@ private int logRunfilesTree(
             } else {
               symlinkTarget.setUnresolvedSymlinkId(logUnresolvedSymlink(artifact, path));
             }
+            builder.putSymlinks(relativePath.getPathString(), symlinkTarget.build());
+          }
+
+          var emptyFilenames = runfilesTree.getEmptyFilenamesForLogging();
+          if (!emptyFilenames.isEmpty()) {
+            // This case is rare: it only applies to Python runfiles and only with
+            // --incompatible_default_to_explicit_init_py. We optimize for the common case and thus
+            // have to copy and sort the symlinks map here.
+            var symlinks = new TreeMap<>(builder.getSymlinksMap());
+            for (String emptyFilename : emptyFilenames.toList()) {
+              symlinks.put(
+                  PathFragment.create(workspaceName).getRelative(emptyFilename).getPathString(),
+                  ExecLogEntry.RunfilesTree.SymlinkTarget.newBuilder()
+                      .setEmptyFile(Empty.getDefaultInstance())
+                      .build());
+            }
+            builder.clearSymlinks();
+            builder.putAllSymlinks(symlinks);
           }
 
           return ExecLogEntry.newBuilder().setRunfilesTree(builder);
diff --git a/src/main/java/com/google/devtools/build/lib/exec/SpawnLogReconstructor.java b/src/main/java/com/google/devtools/build/lib/exec/SpawnLogReconstructor.java
index 22efbafe8639d9..85cecc7307ee4a 100644
--- a/src/main/java/com/google/devtools/build/lib/exec/SpawnLogReconstructor.java
+++ b/src/main/java/com/google/devtools/build/lib/exec/SpawnLogReconstructor.java
@@ -14,19 +14,16 @@
 package com.google.devtools.build.lib.exec;
 
 import static com.google.common.collect.ImmutableList.toImmutableList;
-import static com.google.common.collect.ImmutableSet.toImmutableSet;
 
 import com.github.luben.zstd.ZstdInputStream;
 import com.google.common.collect.ImmutableList;
 import com.google.common.collect.Iterables;
-import com.google.devtools.build.lib.bazel.rules.python.BazelPyBuiltins;
 import com.google.devtools.build.lib.cmdline.LabelConstants;
 import com.google.devtools.build.lib.exec.Protos.ExecLogEntry;
 import com.google.devtools.build.lib.exec.Protos.File;
 import com.google.devtools.build.lib.exec.Protos.SpawnExec;
 import com.google.devtools.build.lib.util.Pair;
 import com.google.devtools.build.lib.util.io.MessageInputStream;
-import com.google.devtools.build.lib.vfs.PathFragment;
 import java.io.IOException;
 import java.io.InputStream;
 import java.util.ArrayDeque;
@@ -35,7 +32,6 @@
 import java.util.HashSet;
 import java.util.LinkedHashMap;
 import java.util.Map;
-import java.util.Set;
 import java.util.SortedMap;
 import java.util.SortedSet;
 import java.util.TreeMap;
@@ -240,25 +236,13 @@ private Pair<String, Collection<File>> reconstructRunfilesDir(
     inputs.stream()
         .flatMap(
             file ->
-                getRunfilesPaths(file.getPath())
+                getRunfilesPaths(file.getPath(), runfilesTree.getLegacyExternalRunfiles())
                     .map(
                         relativePath ->
                             file.toBuilder()
                                 .setPath(runfilesTree.getPath() + "/" + relativePath)
                                 .build()))
         .forEach(file -> builder.put(file.getPath(), file));
-    if (runfilesTree.getCreateInitPy()) {
-      Set<PathFragment> manifest =
-          Stream.concat(
-                  runfilesTree.getSymlinksMap().keySet().stream(),
-                  inputs.stream().flatMap(file -> getRunfilesPaths(file.getPath())))
-              .map(PathFragment::create)
-              .collect(toImmutableSet());
-      for (PathFragment emptyFilePath : BazelPyBuiltins.GET_INIT_PY_FILES.getExtraPaths(manifest)) {
-        String path = runfilesTree.getPath() + "/" + emptyFilePath.getPathString();
-        builder.put(path, File.newBuilder().setPath(path).build());
-      }
-    }
     String workspaceDir = runfilesTree.getPath() + "/" + workspaceRunfilesDirectory + "/";
     if (builder.keySet().stream().noneMatch(p -> p.startsWith(workspaceDir))) {
       String emptyRunfile = workspaceDir + ".runfile";
@@ -267,7 +251,7 @@ private Pair<String, Collection<File>> reconstructRunfilesDir(
     return Pair.of(runfilesTree.getPath(), ImmutableList.copyOf(builder.values()));
   }
 
-  private Stream<String> getRunfilesPaths(String originalPath) {
+  private Stream<String> getRunfilesPaths(String originalPath, boolean legacyExternalRunfiles) {
     String path = originalPath;
     if (path.startsWith("bazel-out/") || path.startsWith("blaze-out/")) {
       // Trim the first three segments ("bazel-out/<config>/bin/") from the path.
@@ -275,10 +259,12 @@ private Stream<String> getRunfilesPaths(String originalPath) {
       path = path.substring(thirdSlash + 1);
     }
     if (path.startsWith(LabelConstants.EXTERNAL_PATH_PREFIX.getPathString())) {
-      return Stream.of(
-          path.substring(LabelConstants.EXTERNAL_PATH_PREFIX.getPathString().length()),
-          // --legacy_external_runfiles
-          workspaceRunfilesDirectory + "/" + path);
+      Stream.Builder<String> paths = Stream.builder();
+      paths.add(path.substring(LabelConstants.EXTERNAL_PATH_PREFIX.getPathString().length()));
+      if (legacyExternalRunfiles) {
+        paths.add(workspaceRunfilesDirectory + "/" + path);
+      }
+      return paths.build();
     }
     return Stream.of(workspaceRunfilesDirectory + "/" + path);
   }
@@ -286,6 +272,7 @@ private Stream<String> getRunfilesPaths(String originalPath) {
   private Collection<File> reconstructRunfilesSymlinkTarget(
       String newPath, ExecLogEntry.RunfilesTree.SymlinkTarget target) throws IOException {
     return switch (target.getTargetCase()) {
+      case EMPTY_FILE -> ImmutableList.of(File.newBuilder().setPath(newPath).build());
       case FILE_ID -> {
         var file = getFromMap(fileMap, target.getFileId());
         yield ImmutableList.of(file.toBuilder().setPath(newPath).build());
diff --git a/src/main/protobuf/BUILD b/src/main/protobuf/BUILD
index 177d778bde7322..e96a6428287cb9 100644
--- a/src/main/protobuf/BUILD
+++ b/src/main/protobuf/BUILD
@@ -316,6 +316,7 @@ proto_library(
     srcs = ["spawn.proto"],
     deps = [
         "@com_google_protobuf//:duration_proto",
+        "@com_google_protobuf//:empty_proto",
         "@com_google_protobuf//:timestamp_proto",
     ],
 )
diff --git a/src/main/protobuf/spawn.proto b/src/main/protobuf/spawn.proto
index d24661a0eb73f3..969a78013f1f0b 100644
--- a/src/main/protobuf/spawn.proto
+++ b/src/main/protobuf/spawn.proto
@@ -17,6 +17,7 @@ syntax = "proto3";
 package tools.protos;
 
 import "google/protobuf/duration.proto";
+import "google/protobuf/empty.proto";
 import "google/protobuf/timestamp.proto";
 
 option java_package = "com.google.devtools.build.lib.exec";
@@ -263,6 +264,7 @@ message ExecLogEntry {
         int32 file_id = 1;
         int32 directory_id = 2;
         int32 unresolved_symlink_id = 3;
+        google.protobuf.Empty empty_file = 4;
       }
     }
 
@@ -287,7 +289,7 @@ message ExecLogEntry {
     // The artifacts in the runfiles tree that are symlinked at custom
     // locations.
     map<string, SymlinkTarget> symlinks = 3;
-    bool create_init_py = 4;
+    bool legacy_external_runfiles = 4;
   }
 
   // A set of spawn inputs.
diff --git a/src/test/java/com/google/devtools/build/lib/analysis/util/FakeRunfilesTree.java b/src/test/java/com/google/devtools/build/lib/analysis/util/FakeRunfilesTree.java
index 084cbbd9b4704a..f063f0fa02b697 100644
--- a/src/test/java/com/google/devtools/build/lib/analysis/util/FakeRunfilesTree.java
+++ b/src/test/java/com/google/devtools/build/lib/analysis/util/FakeRunfilesTree.java
@@ -100,4 +100,14 @@ public NestedSet<Artifact> getArtifactsAtCanonicalLocationsForLogging() {
   public Map<PathFragment, Artifact> getAllSymlinksForLogging() {
     return runfiles.getAllSymlinksForLogging(repoMappingManifest);
   }
+
+  @Override
+  public NestedSet<String> getEmptyFilenamesForLogging() {
+    return runfiles.getEmptyFilenames();
+  }
+
+  @Override
+  public boolean isLegacyExternalRunfiles() {
+    return runfiles.isLegacyExternalRunfiles();
+  }
 }
diff --git a/src/test/java/com/google/devtools/build/lib/exec/BUILD b/src/test/java/com/google/devtools/build/lib/exec/BUILD
index cb7d1b1ac63210..783982388a3a35 100644
--- a/src/test/java/com/google/devtools/build/lib/exec/BUILD
+++ b/src/test/java/com/google/devtools/build/lib/exec/BUILD
@@ -52,11 +52,10 @@ java_library(
         "//src/main/java/com/google/devtools/build/lib/exec:spawn_exec_exception",
         "//src/main/java/com/google/devtools/build/lib/exec:spawn_input_expander",
         "//src/main/java/com/google/devtools/build/lib/exec:spawn_log_context",
-        "//src/main/java/com/google/devtools/build/lib/exec:spawn_log_reconstructor",
+        "//src/main/java/com/google/devtools/build/lib/exec:spawn_log_context_utils",
         "//src/main/java/com/google/devtools/build/lib/exec:spawn_runner",
         "//src/main/java/com/google/devtools/build/lib/exec:spawn_strategy_policy",
         "//src/main/java/com/google/devtools/build/lib/exec:spawn_strategy_registry",
-        "//src/main/java/com/google/devtools/build/lib/exec:stable_sort",
         "//src/main/java/com/google/devtools/build/lib/exec:standalone_test_result",
         "//src/main/java/com/google/devtools/build/lib/exec:standalone_test_strategy",
         "//src/main/java/com/google/devtools/build/lib/exec:streamed_test_output",
diff --git a/src/test/java/com/google/devtools/build/lib/exec/SpawnLogContextTestBase.java b/src/test/java/com/google/devtools/build/lib/exec/SpawnLogContextTestBase.java
index 65a834308e1ecc..314bbf83fc6b40 100644
--- a/src/test/java/com/google/devtools/build/lib/exec/SpawnLogContextTestBase.java
+++ b/src/test/java/com/google/devtools/build/lib/exec/SpawnLogContextTestBase.java
@@ -419,13 +419,7 @@ public void testRunfilesEmptyInput() throws Exception {
     Artifact runfilesMiddleman = ActionsTestUtil.createArtifact(middlemanDir, "runfiles");
     Artifact runfilesInput = ActionsTestUtil.createArtifact(rootDir, "sub/dir/script.py");
     PathFragment runfilesRoot = outputDir.getExecPath().getRelative("foo.runfiles");
-    RunfilesTree runfilesTree =
-        createRunfilesTree(
-            runfilesRoot,
-            ImmutableMap.of(),
-            ImmutableMap.of(),
-            /* createEmptyFiles= */ true,
-            runfilesInput);
+    RunfilesTree runfilesTree = createRunfilesTree(runfilesRoot, runfilesInput);
 
     writeFile(runfilesInput, "abc");
 
@@ -1004,17 +998,18 @@ protected static SpawnExec.Builder defaultSpawnExecBuilder() {
   }
 
   protected static RunfilesTree createRunfilesTree(PathFragment root, Artifact... artifacts) {
-    return createRunfilesTree(root, ImmutableMap.of(), ImmutableMap.of(), false, artifacts);
+    return createRunfilesTree(
+        root, ImmutableMap.of(), ImmutableMap.of(), /* legacyExternalRunfiles= */ false, artifacts);
   }
 
   protected static RunfilesTree createRunfilesTree(
       PathFragment root,
       Map<String, Artifact> symlinks,
       Map<String, Artifact> rootSymlinks,
-      boolean createEmptyFiles,
+      boolean legacyExternalRunfiles,
       Artifact... artifacts) {
     Runfiles.Builder runfiles =
-        new Runfiles.Builder(TestConstants.WORKSPACE_NAME, /* legacyExternalRunfiles= */ true);
+        new Runfiles.Builder(TestConstants.WORKSPACE_NAME, legacyExternalRunfiles);
     runfiles.addArtifacts(Arrays.asList(artifacts));
     for (Map.Entry<String, Artifact> entry : symlinks.entrySet()) {
       runfiles.addSymlink(PathFragment.create(entry.getKey()), entry.getValue());
@@ -1022,9 +1017,7 @@ protected static RunfilesTree createRunfilesTree(
     for (Map.Entry<String, Artifact> entry : rootSymlinks.entrySet()) {
       runfiles.addRootSymlink(PathFragment.create(entry.getKey()), entry.getValue());
     }
-    if (createEmptyFiles) {
-      runfiles.setEmptyFilesSupplier(BazelPyBuiltins.GET_INIT_PY_FILES);
-    }
+    runfiles.setEmptyFilesSupplier(BazelPyBuiltins.GET_INIT_PY_FILES);
     return new RunfilesSupport.RunfilesTreeImpl(root, runfiles.build());
   }
 
diff --git a/src/tools/execlog/src/main/java/com/google/devtools/build/execlog/BUILD b/src/tools/execlog/src/main/java/com/google/devtools/build/execlog/BUILD
index 8bbec35fd044bb..e87e67acb563ee 100644
--- a/src/tools/execlog/src/main/java/com/google/devtools/build/execlog/BUILD
+++ b/src/tools/execlog/src/main/java/com/google/devtools/build/execlog/BUILD
@@ -31,7 +31,7 @@ java_library(
         "ExecLogConverter.java",
     ],
     deps = [
-        "//src/main/java/com/google/devtools/build/lib/exec:spawn_log_reconstructor",
+        "//src/main/java/com/google/devtools/build/lib/exec:spawn_log_context_utils",
         "//src/main/java/com/google/devtools/build/lib/util/io:io-proto",
         "//src/main/java/com/google/devtools/common/options",
         "//src/main/protobuf:spawn_java_proto",