diff --git a/MODULE.bazel b/MODULE.bazel
index 01bad255c..96b30073f 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -90,7 +90,7 @@ new_git_repository = use_repo_rule("@bazel_tools//tools/build_defs/repo:git.bzl"
 new_git_repository(
     name = "tinyusb",
     build_file = "//src/rp2_common/tinyusb:tinyusb.BUILD",
-    commit = "4232642899362fa5e9cf0dc59bad6f1f6d32c563",  # keep-in-sync-with-submodule: tinyusb
+    commit = "4232642899362fa5e9cf0dc59bad6f1f6d32c563",  # keep-in-sync-with-submodule: lib/tinyusb
     remote = "https://github.com/hathach/tinyusb.git",
 )
 
@@ -98,7 +98,7 @@ new_git_repository(
 new_git_repository(
     name = "btstack",
     build_file = "//src/rp2_common/pico_btstack:btstack.BUILD",
-    commit = "2b49e57bd1fae85ac32ac1f41cdb7c794de335f6",  # keep-in-sync-with-submodule: btstack
+    commit = "2b49e57bd1fae85ac32ac1f41cdb7c794de335f6",  # keep-in-sync-with-submodule: lib/btstack
     remote = "https://github.com/bluekitchen/btstack.git",
 )
 
@@ -106,7 +106,7 @@ new_git_repository(
 new_git_repository(
     name = "cyw43-driver",
     build_file = "//src/rp2_common/pico_cyw43_driver:cyw43-driver.BUILD",
-    commit = "cf924bb04c8984675ca0fc2178f082e404e048c3",  # keep-in-sync-with-submodule: cyw43-driver
+    commit = "cf924bb04c8984675ca0fc2178f082e404e048c3",  # keep-in-sync-with-submodule: lib/cyw43-driver
     remote = "https://github.com/georgerobotics/cyw43-driver.git",
 )
 
@@ -114,7 +114,7 @@ new_git_repository(
 new_git_repository(
     name = "lwip",
     build_file = "//src/rp2_common/pico_lwip:lwip.BUILD",
-    commit = "0a0452b2c39bdd91e252aef045c115f88f6ca773",  # keep-in-sync-with-submodule: lwip
+    commit = "0a0452b2c39bdd91e252aef045c115f88f6ca773",  # keep-in-sync-with-submodule: lib/lwip
     remote = "https://github.com/lwip-tcpip/lwip.git",
 )
 
diff --git a/tools/compare_build_systems.py b/tools/compare_build_systems.py
index 01b808313..d24267783 100755
--- a/tools/compare_build_systems.py
+++ b/tools/compare_build_systems.py
@@ -239,7 +239,7 @@ def CompareExternalDependencyVersions():
                 continue
 
             current_submodule_pin = subprocess.run(
-                ("git", "-C", SDK_ROOT, "rev-parse", f'HEAD:lib/{maybe_match.group("dependency")}'),
+                ("git", "-C", SDK_ROOT, "rev-parse", f'HEAD:{maybe_match.group("dependency")}'),
                 text=True,
                 check=True,
                 capture_output=True,