diff --git a/MODULE.bazel b/MODULE.bazel
index fedbefea3..0a49800cd 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -6,13 +6,12 @@ bazel_dep(name = "rules_jvm_external", version = "7.0")
 bazel_dep(name = "aspect_rules_lint", version = "2.5.2")
 bazel_dep(name = "buildifier_prebuilt", version = "8.5.1.2")
 
-JOERN_VERSION = "db325972fdf72e53f76beba77b72e84b2c469905"
+BAZEL_TOOLING_VERSION = "a07fda4f8bc736081ad9921831bc9973e77e6e19"
 
 git_override(
     module_name = "bazel_tooling",
-    commit = "{}".format(JOERN_VERSION),
-    remote = "git@github.com:joernio/joern.git",
-    strip_prefix = "bazel/tooling",
+    commit = "{}".format(BAZEL_TOOLING_VERSION),
+    remote = "git@github.com:joernio/bazel_tooling.git",
 )
 
 bazel_dep(name = "rules_scala", version = "7.2.4")
diff --git a/bazel/java.bzl b/bazel/java.bzl
index 9498929d4..9bb02b445 100644
--- a/bazel/java.bzl
+++ b/bazel/java.bzl
@@ -9,6 +9,8 @@ _rules = make_java_rules(
         "-Xlint:-cast",
         "-XepDisableAllChecks",
     ],
+    common_java_binary_runtime_deps = [],
+    common_java_test_runtime_deps = [],
 )
 
 java_library = _rules.java_library
diff --git a/bazel/scala.bzl b/bazel/scala.bzl
index 813d59ac6..a7655381f 100644
--- a/bazel/scala.bzl
+++ b/bazel/scala.bzl
@@ -11,7 +11,8 @@ _rules = make_scala_rules(
         "-deprecation",
         "-Wconf:msg=Implicit parameters should be provided with a `using` clause:s",
     ],
-    common_scalatest_runtime_deps = [],
+    common_scala_binary_runtime_deps = [],
+    common_scala_test_runtime_deps = [],
 )
 
 scala_library = _rules.scala_library
diff --git a/codepropertygraph/BUILD b/codepropertygraph/BUILD
index bd7862e46..88a5064cc 100644
--- a/codepropertygraph/BUILD
+++ b/codepropertygraph/BUILD
@@ -8,7 +8,7 @@ scala_library(
     ]),
     visibility = ["//visibility:public"],
     deps = [
-        "//schema:domainClasses",
+        "//schema:domainClassesNeverLinked",
         "//schema:java_proto",
         "@maven//:com_google_protobuf_protobuf_java",
         "@maven//:io_joern_flatgraph_core_3",
diff --git a/schema/BUILD b/schema/BUILD
index ffaa0fc22..9686f1031 100644
--- a/schema/BUILD
+++ b/schema/BUILD
@@ -83,7 +83,19 @@ genrule(
 )
 
 java_import(
-    name = "domainClasses",
+    name = "domainClassesNeverLinked",
+    jars = [":domainClasses_jar"],
+    srcjar = ":domainClasses_src_jar",
+    visibility = ["//visibility:public"],
+    exports = [
+        "@maven//:io_joern_flatgraph_core_3",
+        "@maven//:io_joern_flatgraph_help_3",
+    ],
+    neverlink = True,
+)
+
+java_import(
+    name = "domainClassesLinked",
     jars = [":domainClasses_jar"],
     srcjar = ":domainClasses_src_jar",
     visibility = ["//visibility:public"],
diff --git a/schema2json/BUILD b/schema2json/BUILD
index 6290e27dd..9a3c09cee 100644
--- a/schema2json/BUILD
+++ b/schema2json/BUILD
@@ -12,4 +12,7 @@ scala_binary(
         "@maven//:org_json4s_json4s_ast_3",
         "@maven//:org_json4s_json4s_native_3",
     ],
+    runtime_deps = [
+        "//schema:domainClassesLinked",
+    ],
 )