diff --git a/tools/bash/runfiles/runfiles.bash b/tools/bash/runfiles/runfiles.bash
index 6607317c759ab8..540eb90d21461d 100644
--- a/tools/bash/runfiles/runfiles.bash
+++ b/tools/bash/runfiles/runfiles.bash
@@ -142,7 +142,10 @@ function rlocation() {
 
   if [[ -f "$RUNFILES_REPO_MAPPING" ]]; then
     local -r target_repo_apparent_name=$(echo "$1" | cut -d / -f 1)
-    local -r remainder=$(echo "$1" | cut -d / -f 2-)
+     # Use -s to get an empty remainder if the argument does not contain a slash.
+    # The repo mapping should not be applied to single segment paths, which may
+    # be root symlinks.
+    local -r remainder=$(echo "$1" | cut -s -d / -f 2-)
     if [[ -n "$remainder" ]]; then
       if [[ -z "${2+x}" ]]; then
         local -r source_repo=$(runfiles_current_repository 2)
diff --git a/tools/bash/runfiles/runfiles_test.bash b/tools/bash/runfiles/runfiles_test.bash
index 1e1c096b29e9cd..d9c384787a9462 100755
--- a/tools/bash/runfiles/runfiles_test.bash
+++ b/tools/bash/runfiles/runfiles_test.bash
@@ -216,10 +216,12 @@ function test_directory_based_runfiles_with_repo_mapping_from_main() {
   export RUNFILES_DIR=${tmpdir}/mock/runfiles
   mkdir -p "$RUNFILES_DIR"
   cat > "$RUNFILES_DIR/_repo_mapping" <<EOF
+,config.json,config.json~1.2.3
 ,my_module,_main
 ,my_protobuf,protobuf~3.19.2
 ,my_workspace,_main
 protobuf~3.19.2,protobuf,protobuf~3.19.2
+protobuf~3.19.2,config.json,config.json~1.2.3
 EOF
   export RUNFILES_MANIFEST_FILE=
   source "$runfiles_lib_path"
@@ -258,10 +260,12 @@ function test_directory_based_runfiles_with_repo_mapping_from_other_repo() {
   export RUNFILES_DIR=${tmpdir}/mock/runfiles
   mkdir -p "$RUNFILES_DIR"
   cat > "$RUNFILES_DIR/_repo_mapping" <<EOF
+,config.json,config.json~1.2.3
 ,my_module,_main
 ,my_protobuf,protobuf~3.19.2
 ,my_workspace,_main
 protobuf~3.19.2,protobuf,protobuf~3.19.2
+protobuf~3.19.2,config.json,config.json~1.2.3
 EOF
   export RUNFILES_MANIFEST_FILE=
   source "$runfiles_lib_path"
@@ -296,10 +300,12 @@ function test_manifest_based_runfiles_with_repo_mapping_from_main() {
   local tmpdir="$(mktemp -d $TEST_TMPDIR/tmp.XXXXXXXX)"
 
   cat > "$tmpdir/foo.repo_mapping" <<EOF
+,config.json,config.json~1.2.3
 ,my_module,_main
 ,my_protobuf,protobuf~3.19.2
 ,my_workspace,_main
 protobuf~3.19.2,protobuf,protobuf~3.19.2
+protobuf~3.19.2,config.json,config.json~1.2.3
 EOF
   export RUNFILES_DIR=
   export RUNFILES_MANIFEST_FILE="$tmpdir/foo.runfiles_manifest"
@@ -344,10 +350,12 @@ function test_manifest_based_runfiles_with_repo_mapping_from_other_repo() {
   local tmpdir="$(mktemp -d $TEST_TMPDIR/tmp.XXXXXXXX)"
 
   cat > "$tmpdir/foo.repo_mapping" <<EOF
+,config.json,config.json~1.2.3
 ,my_module,_main
 ,my_protobuf,protobuf~3.19.2
 ,my_workspace,_main
 protobuf~3.19.2,protobuf,protobuf~3.19.2
+protobuf~3.19.2,config.json,config.json~1.2.3
 EOF
   export RUNFILES_DIR=
   export RUNFILES_MANIFEST_FILE="$tmpdir/foo.runfiles_manifest"
diff --git a/tools/cpp/runfiles/runfiles_test.cc b/tools/cpp/runfiles/runfiles_test.cc
index 4abb19f31ef0aa..122b184cafe1d0 100644
--- a/tools/cpp/runfiles/runfiles_test.cc
+++ b/tools/cpp/runfiles/runfiles_test.cc
@@ -586,10 +586,12 @@ TEST_F(RunfilesTest, PathsFromEnvVars) {
 
 TEST_F(RunfilesTest, ManifestBasedRlocationWithRepoMapping_fromMain) {
   string uid = LINE_AS_STRING();
-  unique_ptr<MockFile> rm(MockFile::Create(
-      "foo" + uid + ".repo_mapping",
-      {",my_module,_main", ",my_protobuf,protobuf~3.19.2",
-       ",my_workspace,_main", "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
+  unique_ptr<MockFile> rm(
+      MockFile::Create("foo" + uid + ".repo_mapping",
+                       {",config.json,config.json~1.2.3", ",my_module,_main",
+                        ",my_protobuf,protobuf~3.19.2", ",my_workspace,_main",
+                        "protobuf~3.19.2,config.json,config.json~1.2.3",
+                        "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
   ASSERT_TRUE(rm != nullptr);
   unique_ptr<MockFile> mf(MockFile::Create(
       "foo" + uid + ".runfiles_manifest",
@@ -644,10 +646,12 @@ TEST_F(RunfilesTest, ManifestBasedRlocationWithRepoMapping_fromMain) {
 
 TEST_F(RunfilesTest, ManifestBasedRlocationWithRepoMapping_fromOtherRepo) {
   string uid = LINE_AS_STRING();
-  unique_ptr<MockFile> rm(MockFile::Create(
-      "foo" + uid + ".repo_mapping",
-      {",my_module,_main", ",my_protobuf,protobuf~3.19.2",
-       ",my_workspace,_main", "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
+  unique_ptr<MockFile> rm(
+      MockFile::Create("foo" + uid + ".repo_mapping",
+                       {",config.json,config.json~1.2.3", ",my_module,_main",
+                        ",my_protobuf,protobuf~3.19.2", ",my_workspace,_main",
+                        "protobuf~3.19.2,config.json,config.json~1.2.3",
+                        "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
   ASSERT_TRUE(rm != nullptr);
   unique_ptr<MockFile> mf(MockFile::Create(
       "foo" + uid + ".runfiles_manifest",
@@ -699,10 +703,12 @@ TEST_F(RunfilesTest, ManifestBasedRlocationWithRepoMapping_fromOtherRepo) {
 
 TEST_F(RunfilesTest, DirectoryBasedRlocationWithRepoMapping_fromMain) {
   string uid = LINE_AS_STRING();
-  unique_ptr<MockFile> rm(MockFile::Create(
-      "foo" + uid + ".runfiles/_repo_mapping",
-      {",my_module,_main", ",my_protobuf,protobuf~3.19.2",
-       ",my_workspace,_main", "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
+  unique_ptr<MockFile> rm(
+      MockFile::Create("foo" + uid + ".runfiles/_repo_mapping",
+                       {",config.json,config.json~1.2.3", ",my_module,_main",
+                        ",my_protobuf,protobuf~3.19.2", ",my_workspace,_main",
+                        "protobuf~3.19.2,config.json,config.json~1.2.3",
+                        "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
   ASSERT_TRUE(rm != nullptr);
   string dir = rm->DirName();
   string argv0(dir.substr(0, dir.size() - string(".runfiles").size()));
@@ -746,10 +752,12 @@ TEST_F(RunfilesTest, DirectoryBasedRlocationWithRepoMapping_fromMain) {
 
 TEST_F(RunfilesTest, DirectoryBasedRlocationWithRepoMapping_fromOtherRepo) {
   string uid = LINE_AS_STRING();
-  unique_ptr<MockFile> rm(MockFile::Create(
-      "foo" + uid + ".runfiles/_repo_mapping",
-      {",my_module,_main", ",my_protobuf,protobuf~3.19.2",
-       ",my_workspace,_main", "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
+  unique_ptr<MockFile> rm(
+      MockFile::Create("foo" + uid + ".runfiles/_repo_mapping",
+                       {",config.json,config.json~1.2.3", ",my_module,_main",
+                        ",my_protobuf,protobuf~3.19.2", ",my_workspace,_main",
+                        "protobuf~3.19.2,config.json,config.json~1.2.3",
+                        "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
   ASSERT_TRUE(rm != nullptr);
   string dir = rm->DirName();
   string argv0(dir.substr(0, dir.size() - string(".runfiles").size()));
@@ -790,10 +798,12 @@ TEST_F(RunfilesTest, DirectoryBasedRlocationWithRepoMapping_fromOtherRepo) {
 TEST_F(RunfilesTest,
        DirectoryBasedRlocationWithRepoMapping_fromOtherRepo_withSourceRepo) {
   string uid = LINE_AS_STRING();
-  unique_ptr<MockFile> rm(MockFile::Create(
-      "foo" + uid + ".runfiles/_repo_mapping",
-      {",my_module,_main", ",my_protobuf,protobuf~3.19.2",
-       ",my_workspace,_main", "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
+  unique_ptr<MockFile> rm(
+      MockFile::Create("foo" + uid + ".runfiles/_repo_mapping",
+                       {",config.json,config.json~1.2.3", ",my_module,_main",
+                        ",my_protobuf,protobuf~3.19.2", ",my_workspace,_main",
+                        "protobuf~3.19.2,config.json,config.json~1.2.3",
+                        "protobuf~3.19.2,protobuf,protobuf~3.19.2"}));
   ASSERT_TRUE(rm != nullptr);
   string dir = rm->DirName();
   string argv0(dir.substr(0, dir.size() - string(".runfiles").size()));
diff --git a/tools/java/runfiles/testing/RunfilesTest.java b/tools/java/runfiles/testing/RunfilesTest.java
index 8b88ce28bd4e3d..92d420f77ce7bf 100644
--- a/tools/java/runfiles/testing/RunfilesTest.java
+++ b/tools/java/runfiles/testing/RunfilesTest.java
@@ -264,9 +264,11 @@ public void testManifestBasedRlocationWithRepoMapping_fromMain() throws Exceptio
         tempFile(
             "foo.repo_mapping",
             ImmutableList.of(
+                ",config.json,config.json~1.2.3",
                 ",my_module,_main",
                 ",my_protobuf,protobuf~3.19.2",
                 ",my_workspace,_main",
+                "protobuf~3.19.2,config.json,config.json~1.2.3",
                 "protobuf~3.19.2,protobuf,protobuf~3.19.2"));
     Path mf =
         tempFile(
@@ -318,9 +320,11 @@ public void testManifestBasedRlocationUnmapped() throws Exception {
         tempFile(
             "foo.repo_mapping",
             ImmutableList.of(
+                ",config.json,config.json~1.2.3",
                 ",my_module,_main",
                 ",my_protobuf,protobuf~3.19.2",
                 ",my_workspace,_main",
+                "protobuf~3.19.2,config.json,config.json~1.2.3",
                 "protobuf~3.19.2,protobuf,protobuf~3.19.2"));
     Path mf =
         tempFile(
@@ -367,9 +371,11 @@ public void testManifestBasedRlocationWithRepoMapping_fromOtherRepo() throws Exc
         tempFile(
             "foo.repo_mapping",
             ImmutableList.of(
+                ",config.json,config.json~1.2.3",
                 ",my_module,_main",
                 ",my_protobuf,protobuf~3.19.2",
                 ",my_workspace,_main",
+                "protobuf~3.19.2,config.json,config.json~1.2.3",
                 "protobuf~3.19.2,protobuf,protobuf~3.19.2"));
     Path mf =
         tempFile(
@@ -419,9 +425,11 @@ public void testDirectoryBasedRlocationWithRepoMapping_fromMain() throws Excepti
         tempFile(
             dir.resolve("_repo_mapping").toString(),
             ImmutableList.of(
+                ",config.json,config.json~1.2.3",
                 ",my_module,_main",
                 ",my_protobuf,protobuf~3.19.2",
                 ",my_workspace,_main",
+                "protobuf~3.19.2,config.json,config.json~1.2.3",
                 "protobuf~3.19.2,protobuf,protobuf~3.19.2"));
     Runfiles r = Runfiles.createDirectoryBasedForTesting(dir.toString()).withSourceRepository("");
 
@@ -458,9 +466,11 @@ public void testDirectoryBasedRlocationUnmapped() throws Exception {
         tempFile(
             dir.resolve("_repo_mapping").toString(),
             ImmutableList.of(
+                ",config.json,config.json~1.2.3",
                 ",my_module,_main",
                 ",my_protobuf,protobuf~3.19.2",
                 ",my_workspace,_main",
+                "protobuf~3.19.2,config.json,config.json~1.2.3",
                 "protobuf~3.19.2,protobuf,protobuf~3.19.2"));
     Runfiles r = Runfiles.createDirectoryBasedForTesting(dir.toString()).unmapped();
 
@@ -497,9 +507,11 @@ public void testDirectoryBasedRlocationWithRepoMapping_fromOtherRepo() throws Ex
         tempFile(
             dir.resolve("_repo_mapping").toString(),
             ImmutableList.of(
+                ",config.json,config.json~1.2.3",
                 ",my_module,_main",
                 ",my_protobuf,protobuf~3.19.2",
                 ",my_workspace,_main",
+                "protobuf~3.19.2,config.json,config.json~1.2.3",
                 "protobuf~3.19.2,protobuf,protobuf~3.19.2"));
     Runfiles r =
         Runfiles.createDirectoryBasedForTesting(dir.toString())