diff --git a/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java b/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java
index 53e6494656..22261cd268 100644
--- a/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java
+++ b/src/main/java/com/google/devtools/build/lib/rules/repository/RepositoryDelegatorFunction.java
@@ -55,6 +55,7 @@ import com.google.devtools.build.skyframe.SkyFunctionException.Transience;
 import com.google.devtools.build.skyframe.SkyKey;
 import com.google.devtools.build.skyframe.SkyValue;
 import java.io.IOException;
+import java.util.Collections;
 import java.util.Map;
 import java.util.Optional;
 import java.util.TreeMap;
@@ -193,16 +194,16 @@ public final class RepositoryDelegatorFunction implements SkyFunction {
       }

       if (shouldUseCachedRepos(env, handler, repoRoot, rule)) {
-        // Make sure marker file is up-to-date; correctly describes the current repository state
-        byte[] markerHash = digestWriter.areRepositoryAndMarkerFileConsistent(handler, env);
-        if (env.valuesMissing()) {
-          return null;
-        }
-        if (markerHash != null) { // repo exist & up-to-date
+        // Nix hack: Skip marker file validation but only for repos that have
+        // been fully initialized. Check for common root files that indicate a
+        // real repo, not an empty dir created by module extensions before the
+        // repository rule has had a chance to run.
+        if (repoRoot.getChild("BUILD").exists() || repoRoot.getChild("BUILD.bazel").exists()
+            || repoRoot.getChild("WORKSPACE").exists() || repoRoot.getChild("WORKSPACE.bazel").exists()
+            || repoRoot.getChild("MODULE.bazel").exists()) {
           return RepositoryDirectoryValue.builder()
               .setPath(repoRoot)
-              .setDigest(markerHash)
-              .setExcludeFromVendoring(excludeRepoFromVendoring)
+              .setDigest(digestWriter.writeMarkerFile(Collections.emptyMap()))
               .build();
         }
       }
diff --git a/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java b/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java
index 649647c5f2..64d05b530c 100644
--- a/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java
+++ b/src/main/java/com/google/devtools/build/lib/shell/JavaSubprocessFactory.java
@@ -165,7 +165,6 @@ public class JavaSubprocessFactory implements SubprocessFactory {
     }
     builder.command(argv);
     if (params.getEnv() != null) {
-      builder.environment().clear();
       builder.environment().putAll(params.getEnv());
     }