diff --git a/.bazelrc b/.bazelrc
index e2ccb69be902..9abda3e670a0 100644
--- a/.bazelrc
+++ b/.bazelrc
@@ -24,5 +24,6 @@ common --registry=file:///%workspace%/misc/bazel/registry
 common --registry=https://bcr.bazel.build
 
 common --@rules_dotnet//dotnet/settings:strict_deps=false
+common --experimental_isolated_extension_usages
 
 try-import %workspace%/local.bazelrc
diff --git a/.bazelrc.internal b/.bazelrc.internal
index f7718959c9de..dcc8dafa6c7f 100644
--- a/.bazelrc.internal
+++ b/.bazelrc.internal
@@ -8,3 +8,4 @@ common --registry=https://bcr.bazel.build
 # its implementation packages without providing any code itself.
 # We either can depend on internal implementation details, or turn of strict deps.
 common --@rules_dotnet//dotnet/settings:strict_deps=false
+common --experimental_isolated_extension_usages
diff --git a/MODULE.bazel b/MODULE.bazel
index 3352e004375b..d2add26c88d5 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -1,6 +1,7 @@
 module(
-    name = "codeql",
+    name = "ql",
     version = "0.0",
+    repo_name = "codeql",
 )
 
 # this points to our internal repository when `codeql` is checked out as a submodule thereof
@@ -30,11 +31,13 @@ bazel_dep(name = "rules_rust", version = "0.49.1")
 
 bazel_dep(name = "buildifier_prebuilt", version = "6.4.0", dev_dependency = True)
 
-crate = use_extension(
+# crate_py but shortened due to Windows file path considerations
+cp = use_extension(
     "@rules_rust//crate_universe:extension.bzl",
     "crate",
+    isolate = True,
 )
-crate.from_cargo(
+cp.from_cargo(
     name = "py_deps",
     cargo_lockfile = "//python/extractor/tsg-python:Cargo.lock",
     manifests = [
@@ -42,15 +45,23 @@ crate.from_cargo(
         "//python/extractor/tsg-python/tsp:Cargo.toml",
     ],
 )
-crate.from_cargo(
-    name = "ruby_deps",
+use_repo(cp, "py_deps")
+
+# crate_ruby, but shortened due to windows file paths
+r = use_extension(
+    "@rules_rust//crate_universe:extension.bzl",
+    "crate",
+    isolate = True,
+)
+r.from_cargo(
+    name = "rd",
     cargo_lockfile = "//ruby/extractor:Cargo.lock",
     manifests = [
         "//ruby/extractor:Cargo.toml",
         "//ruby/extractor/codeql-extractor-fake-crate:Cargo.toml",
     ],
 )
-use_repo(crate, "py_deps", "ruby_deps")
+use_repo(r, ruby_deps = "rd")
 
 dotnet = use_extension("@rules_dotnet//dotnet:extensions.bzl", "dotnet")
 dotnet.toolchain(dotnet_version = "8.0.101")
diff --git a/misc/bazel/internal/zipmerge/zipmerge_test.cpp b/misc/bazel/internal/zipmerge/zipmerge_test.cpp
index ee30b764a6d2..9bee1a79c02f 100644
--- a/misc/bazel/internal/zipmerge/zipmerge_test.cpp
+++ b/misc/bazel/internal/zipmerge/zipmerge_test.cpp
@@ -75,7 +75,7 @@ std::string get_file(const char* name) {
     return ret;
   }();
   // this works from both `codeql` and the internal repository
-  for (auto prefix : {"_main", "codeql~"}) {
+  for (auto prefix : {"_main", "ql~"}) {
     auto ret = runfiles->Rlocation(prefix + "/misc/bazel/internal/zipmerge/test-files/"s + name);
     if (fs::exists(ret)) {
       return ret;