diff --git a/.bazelrc b/.bazelrc
index e2ccb69be902e..9abda3e670a01 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 f7718959c9de7..dcc8dafa6c7f0 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 3352e004375b8..5f16293101585 100644
--- a/MODULE.bazel
+++ b/MODULE.bazel
@@ -1,5 +1,5 @@
 module(
-    name = "codeql",
+    name = "ql",
     version = "0.0",
 )
 
@@ -30,11 +30,13 @@ 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 +44,23 @@ 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, "rd")
 
 dotnet = use_extension("@rules_dotnet//dotnet:extensions.bzl", "dotnet")
 dotnet.toolchain(dotnet_version = "8.0.101")
diff --git a/java/kotlin-extractor/BUILD.bazel b/java/kotlin-extractor/BUILD.bazel
index f95661f8128c0..49cf5e1664b5a 100644
--- a/java/kotlin-extractor/BUILD.bazel
+++ b/java/kotlin-extractor/BUILD.bazel
@@ -16,7 +16,7 @@ will build a default variant:
 * the version will be taken as the last supported version less than the version of the currently available `kotlinc`,
   or `CODEQL_KOTLIN_SINGLE_VERSION` if set.
 
-If building from the `codeql` repository, `@codeql` can be skipped.
+If building from the `codeql` repository, `@codeql` needs to be skipped.
 
 It is recommended to use the `kotlinc` wrapper in `dev` (which is also available in `tools` from `semmle-code`), which
 takes care about providing a sensible default version and keep the version of the default target up to date.
@@ -32,7 +32,7 @@ version. Possible workarounds for that:
 # This file is used in the `@codeql_kotlin_embeddable` external repo, which means we need to
 # reference explicitly @codeql
 load(
-    "@codeql//java/kotlin-extractor:versions.bzl",
+    "@ql//java/kotlin-extractor:versions.bzl",
     "VERSIONS",
     "get_compatilibity_sources",
     "get_language_version",
@@ -107,7 +107,7 @@ kt_javac_options(
         kt_jvm_library(
             name = "%s-%s" % (_extractor_name_prefix, v),
             srcs =
-                ["@codeql//java/kotlin-extractor:generated-dbscheme"] +
+                ["@ql//java/kotlin-extractor:generated-dbscheme"] +
                 glob(
                     [
                         "src/**/*.kt",
@@ -124,7 +124,7 @@ kt_javac_options(
             kotlinc_opts = ":kotlinc-options-%s" % v,
             module_name = "codeql-kotlin-extractor",
             # resource_strip_prefix is very nit-picky: the following makes it work from
-            # `codeql`, `@codeql_kotlin_embeddable` and `semmle-code`
+            # `ql`, `@codeql_kotlin_embeddable` and `semmle-code`
             resource_strip_prefix = (
                 ("../%s/" % repo_name() if repo_name() else "") +
                 ("%s/" % package_name() if package_name() else "") +
@@ -145,7 +145,7 @@ kt_javac_options(
         # if in main repository, alias the embeddable versions from the modified @codeql_kotlin_embeddable repo
         alias(
             name = "%s-embeddable-%s" % (_common_extractor_name_prefix, v),
-            actual = "@codeql_kotlin_embeddable//:%s-embeddable-%s" % (_common_extractor_name_prefix, v),
+            actual = "@ql//:%s-embeddable-%s" % (_common_extractor_name_prefix, v),
             visibility = ["//visibility:public"],
         ) if not _for_embeddable else None,
     )
@@ -155,7 +155,7 @@ kt_javac_options(
 (
     genrule(
         name = "generated-dbscheme",
-        srcs = ["@codeql//java:dbscheme"],
+        srcs = ["@ql//java:dbscheme"],
         outs = ["KotlinExtractorDbScheme.kt"],
         cmd = "$(execpath :generate_dbscheme) $< $@",
         tools = [":generate_dbscheme"],
diff --git a/ruby/extractor/BUILD.bazel b/ruby/extractor/BUILD.bazel
index e3c2a387af59d..bb39608f3fc13 100644
--- a/ruby/extractor/BUILD.bazel
+++ b/ruby/extractor/BUILD.bazel
@@ -1,4 +1,4 @@
-load("@ruby_deps//:defs.bzl", "aliases", "all_crate_deps")
+load("@rd//:defs.bzl", "aliases", "all_crate_deps")
 load("//misc/bazel:rust.bzl", "codeql_rust_binary")
 
 codeql_rust_binary(
diff --git a/shared/tree-sitter-extractor/BUILD.bazel b/shared/tree-sitter-extractor/BUILD.bazel
index e57a9f47ca139..5d9c4ca1ccf84 100644
--- a/shared/tree-sitter-extractor/BUILD.bazel
+++ b/shared/tree-sitter-extractor/BUILD.bazel
@@ -1,4 +1,4 @@
-load("@ruby_deps//:defs.bzl", "aliases", "all_crate_deps")
+load("@rd//:defs.bzl", "aliases", "all_crate_deps")
 load("@rules_rust//rust:defs.bzl", "rust_library")
 
 package(default_visibility = ["//visibility:public"])