diff --git a/.github/bin/run-clang-format.sh b/.github/bin/run-clang-format.sh
index 33e1116ad..7abc539c8 100755
--- a/.github/bin/run-clang-format.sh
+++ b/.github/bin/run-clang-format.sh
@@ -37,7 +37,7 @@ find . -name "*.h" -o -name "*.cc" \
 # If we have buildifier installed, use that on BUILD files
 if command -v ${BUILDIFIER} >/dev/null; then
   echo "Run $(buildifier --version)"
-  ${BUILDIFIER} -lint=fix WORKSPACE $(find . -name BUILD -o -name "*.bzl")
+  ${BUILDIFIER} -lint=fix WORKSPACE MODULE.bazel $(find . -name BUILD -o -name "*.bzl")
 fi
 
 # Check if we got any diff
diff --git a/MODULE.bazel b/MODULE.bazel
index f1dc33971..e3e6601f7 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -4,74 +4,72 @@ module(
 
 bazel_dep(name = "platforms", version = "0.0.8")
 bazel_dep(name = "bazel_skylib", version = "1.5.0")
-
 bazel_dep(name = "rules_license", version = "0.0.8")
 bazel_dep(name = "rules_proto", version = "6.0.0-rc2")
 bazel_dep(name = "rules_cc", version = "0.0.9")
 
 # Register m4 rules and toolchain.
 bazel_dep(name = "rules_m4", version = "0.2.3")
+
 m4 = use_extension(
     "@rules_m4//m4/extensions:m4_repository_ext.bzl",
     "m4_repository_ext",
 )
 m4.repository(
     name = "m4",
-    version = "1.4.18",
     extra_copts = ["-O3"],
+    version = "1.4.18",
 )
 use_repo(m4, "m4")
+
 register_toolchains("@m4//:toolchain")
 
 # Register bison rules and toolchain.
 bazel_dep(name = "rules_bison", version = "0.2.2")
+
 bison = use_extension(
     "@rules_bison//bison/extensions:bison_repository_ext.bzl",
     "bison_repository_ext",
 )
 bison.repository(
     name = "bison",
-    version = "3.3.2",
     extra_copts = ["-O3"],
+    version = "3.3.2",
 )
 use_repo(bison, "bison")
+
 register_toolchains("@bison//:toolchain")
 
 # Register flex rules and toolchain.
 bazel_dep(name = "rules_flex", version = "0.2.1")
+
 flex = use_extension(
     "@rules_flex//flex/extensions:flex_repository_ext.bzl",
     "flex_repository_ext",
 )
 flex.repository(
     name = "flex",
-    version = "2.6.4",
     extra_copts = ["-O3"],
+    version = "2.6.4",
 )
 use_repo(flex, "flex")
+
 register_toolchains("@flex//:toolchain")
 
 # abseil-cpp can not be updated beyond the following curringly, as newer
 # ones use googletest that is not compatible with bazel 6 anymore.
-bazel_dep(name = "abseil-cpp", version = "20240116.2", repo_name="com_google_absl")
+bazel_dep(name = "abseil-cpp", version = "20240116.2", repo_name = "com_google_absl")
 single_version_override(
     module_name = "abseil-cpp",
     patch_strip = 1,
-    version = "20240116.2",
     patches = ["//bazel:absl.patch"],
+    version = "20240116.2",
 )
 
-# Json module only provide the multi-header target, but that will
-# make misc-inlude-cleaner complain about not direct includes.
-bazel_dep(name = "nlohmann_json", version = "3.11.3", repo_name="jsonhpp")
-single_version_override(
-    module_name = "nlohmann_json",
-    patches = ["//bazel:nlohmann_module.patch"],
-)
-
-bazel_dep(name = "re2", version = "2023-09-01", repo_name="com_googlesource_code_re2")
+bazel_dep(name = "nlohmann_json", version = "3.11.3.bcr.1", repo_name = "jsonhpp")
+bazel_dep(name = "re2", version = "2023-09-01", repo_name = "com_googlesource_code_re2")
 
 # Newer versions require bazel 7, so this is the last we can use currently.
-bazel_dep(name = "googletest", version = "1.14.0.bcr.1", repo_name="com_google_googletest")
-bazel_dep(name = "protobuf", version = "26.0", repo_name="com_google_protobuf")
+bazel_dep(name = "googletest", version = "1.14.0.bcr.1", repo_name = "com_google_googletest")
+bazel_dep(name = "protobuf", version = "26.0", repo_name = "com_google_protobuf")
 bazel_dep(name = "zlib", version = "1.3.1")
diff --git a/bazel/jsonhpp.BUILD b/bazel/jsonhpp.BUILD
index dae48c5f8..21a6ced12 100644
--- a/bazel/jsonhpp.BUILD
+++ b/bazel/jsonhpp.BUILD
@@ -5,7 +5,7 @@ licenses(["unencumbered"])  # Public Domain or MIT
 exports_files(["LICENSE"])
 
 cc_library(
-    name = "json",
+    name = "singleheader-json",
     hdrs = [
         "single_include/nlohmann/json.hpp",
     ],
diff --git a/bazel/nlohmann_module.patch b/bazel/nlohmann_module.patch
deleted file mode 100644
index 9f6ddd231..000000000
--- a/bazel/nlohmann_module.patch
+++ /dev/null
@@ -1,23 +0,0 @@
---- BUILD.bazel	2024-09-27 08:43:50.907170239 -0700
-+++ BUILD.bazel	2024-09-27 08:46:27.441297623 -0700
-@@ -1,5 +1,5 @@
- cc_library(
--    name = "json",
-+    name = "json-multiheader",
-     hdrs = [
-         "include/nlohmann/adl_serializer.hpp",
-         "include/nlohmann/byte_container_with_subtype.hpp",
-@@ -51,3 +51,13 @@
-     visibility = ["//visibility:public"],
-     alwayslink = True,
- )
-+cc_library(
-+    name = "json",
-+    hdrs = [
-+        "single_include/nlohmann/json.hpp",
-+    ],
-+    includes = ["single_include"],
-+    visibility = ["//visibility:public"],
-+    copts = ["-fexceptions"],
-+    features = ["-use_header_modules"],  # precompiled headers incompatible with -fexceptions.
-+)
diff --git a/common/lsp/BUILD b/common/lsp/BUILD
index 8273dc263..c7b520128 100644
--- a/common/lsp/BUILD
+++ b/common/lsp/BUILD
@@ -53,7 +53,7 @@ cc_library(
     deps = [
         "//common/util:logging",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -70,7 +70,7 @@ cc_test(
         "@com_google_absl//absl/strings:string_view",
         "@com_google_googletest//:gtest",
         "@com_google_googletest//:gtest_main",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -85,7 +85,7 @@ genrule(
 cc_library(
     name = "lsp-protocol",
     hdrs = ["lsp-protocol.h"],
-    deps = ["@jsonhpp//:json"],
+    deps = ["@jsonhpp//:singleheader-json"],
 )
 
 cc_library(
@@ -167,7 +167,7 @@ cc_binary(
         "@com_google_absl//absl/status",
         "@com_google_absl//absl/strings",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -181,7 +181,7 @@ cc_binary(
         ":message-stream-splitter",
         "@com_google_absl//absl/status",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -224,7 +224,7 @@ genrule(
 cc_library(
     name = "jcxxgen-testfile",
     hdrs = ["jcxxgen-testfile.h"],
-    deps = ["@jsonhpp//:json"],
+    deps = ["@jsonhpp//:singleheader-json"],
 )
 
 cc_test(
@@ -240,6 +240,6 @@ cc_test(
         "@com_google_absl//absl/strings",
         "@com_google_googletest//:gtest",
         "@com_google_googletest//:gtest_main",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
diff --git a/common/text/BUILD b/common/text/BUILD
index 475db5d5b..89fa06ff1 100644
--- a/common/text/BUILD
+++ b/common/text/BUILD
@@ -37,7 +37,7 @@ cc_library(
     hdrs = ["token_info_json.h"],
     deps = [
         ":token-info",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -415,7 +415,7 @@ cc_test(
         "@com_google_absl//absl/strings:string_view",
         "@com_google_googletest//:gtest",
         "@com_google_googletest//:gtest_main",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
diff --git a/verilog/CST/BUILD b/verilog/CST/BUILD
index 30ff07d94..3ee9d0a9d 100644
--- a/verilog/CST/BUILD
+++ b/verilog/CST/BUILD
@@ -902,7 +902,7 @@ cc_library(
         "//verilog/parser:verilog-token-classifications",
         "//verilog/parser:verilog-token-enum",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -955,6 +955,6 @@ cc_test(
         "//verilog/analysis:verilog-analyzer",
         "@com_google_googletest//:gtest",
         "@com_google_googletest//:gtest_main",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
diff --git a/verilog/analysis/BUILD b/verilog/analysis/BUILD
index f48c1be4e..76c8fc013 100644
--- a/verilog/analysis/BUILD
+++ b/verilog/analysis/BUILD
@@ -75,7 +75,7 @@ cc_library(
         "//common/analysis:file-analyzer",
         "//common/strings:line-column-map",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -132,7 +132,7 @@ cc_test(
         "//common/util:logging",
         "@com_google_googletest//:gtest",
         "@com_google_googletest//:gtest_main",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
diff --git a/verilog/tools/ls/BUILD b/verilog/tools/ls/BUILD
index d218c7f2a..0bac38938 100644
--- a/verilog/tools/ls/BUILD
+++ b/verilog/tools/ls/BUILD
@@ -106,7 +106,7 @@ cc_library(
         "//verilog/parser:verilog-token-enum",
         "@com_google_absl//absl/strings",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -138,7 +138,7 @@ cc_library(
         "//verilog/CST:package",
         "//verilog/CST:seq-block",
         "//verilog/CST:verilog-nonterminals",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -239,7 +239,7 @@ cc_library(
         "@com_google_absl//absl/flags:flag",
         "@com_google_absl//absl/status",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -260,7 +260,7 @@ cc_test(
         "@com_google_absl//absl/strings:string_view",
         "@com_google_googletest//:gtest",
         "@com_google_googletest//:gtest_main",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
 
@@ -312,6 +312,6 @@ cc_test(
         "@com_google_absl//absl/strings:string_view",
         "@com_google_googletest//:gtest",
         "@com_google_googletest//:gtest_main",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )
diff --git a/verilog/tools/syntax/BUILD b/verilog/tools/syntax/BUILD
index 57899bc0b..7a95c1560 100644
--- a/verilog/tools/syntax/BUILD
+++ b/verilog/tools/syntax/BUILD
@@ -39,7 +39,7 @@ cc_binary(
         "@com_google_absl//absl/status",
         "@com_google_absl//absl/strings",
         "@com_google_absl//absl/strings:string_view",
-        "@jsonhpp//:json",
+        "@jsonhpp//:singleheader-json",
     ],
 )