diff --git a/go/BUILD.bazel b/go/BUILD.bazel
index 6c80e7cb258..e0da93475a2 100644
--- a/go/BUILD.bazel
+++ b/go/BUILD.bazel
@@ -1,13 +1,14 @@
 load("@bazel_skylib//rules:native_binary.bzl", "native_binary")
-load("@gazelle//:def.bzl", "gazelle")
 load("@rules_pkg//pkg:install.bzl", "pkg_install")
 load("@rules_pkg//pkg:mappings.bzl", "pkg_attributes", "pkg_filegroup", "pkg_files")
 load("@rules_pkg//pkg:zip.bzl", "pkg_zip")
 load("//:defs.bzl", "codeql_platform")
 
-gazelle(
+native_binary(
     name = "gazelle",
-    extra_args = ["go/extractor"],
+    src = "@gazelle//cmd/gazelle",
+    out = "gazelle.exe",
+    args = ["go/extractor"],
 )
 
 _gen_binaries = [
@@ -24,9 +25,9 @@ py_binary(
     deps = ["@rules_python//python/runfiles"],
 )
 
-# this is an internal copy of the dbscheme to be used by extractor-pack
-# this allows the extractor-pack target to be independent and up-to-date with respect to
-# having run //go:gen to update the checked in files
+# this is an instance of the dbscheme kept in the bazel build tree
+# this allows everything that bazel builds to be up-to-date,
+# independently from whether //go:gen was already run to update the checked in files
 genrule(
     name = "dbscheme",
     outs = ["go.dbscheme"],
@@ -108,12 +109,3 @@ py_binary(
     main = "create_extractor_pack.py",
     deps = ["@rules_python//python/runfiles"],
 )
-
-native_binary(
-    name = "gen-dbscheme",
-    src = "//go/extractor/cli/go-gen-dbscheme",
-    out = "go-gen-dbscheme",
-    args = [
-        "$$BUILD_WORKSPACE_DIRECTORY/go/ql/lib/go.dbscheme",
-    ],
-)
diff --git a/go/gen.py b/go/gen.py
index 0e9005571ea..6f8d47d7096 100644
--- a/go/gen.py
+++ b/go/gen.py
@@ -24,12 +24,18 @@ def options():
 opts = options()
 
 try:
-    workspace_dir = pathlib.Path(os.environ['BUILD_WORKSPACE_DIRECTORY'])
+    workspace_dir = pathlib.Path(os.environ.pop('BUILD_WORKSPACE_DIRECTORY'))
 except KeyError:
     print("this should be run with bazel run", file=sys.stderr)
     sys.exit(1)
 
 go_extractor_dir = workspace_dir / "go" / "extractor"
+
+if not go_extractor_dir.exists():
+    # internal repo?
+    workspace_dir /= "ql"
+    go_extractor_dir = workspace_dir / "go" / "extractor"
+
 go_dbscheme = workspace_dir / "go" / "ql" / "lib" / "go.dbscheme"
 r = runfiles.Create()
 go, gazelle, go_gen_dbscheme = map(r.Rlocation, opts.executables)
@@ -49,8 +55,8 @@ if opts.force:
     for build_file in existing_build_files:
         build_file.unlink()
 
-print("running gazelle")
-subprocess.check_call([gazelle])
+print("running gazelle", gazelle, go_extractor_dir)
+subprocess.check_call([gazelle, "go/extractor"], cwd=workspace_dir)
 
 # we want to stamp all newly generated `BUILD.bazel` files with a header
 build_files_to_update = set(go_extractor_dir.glob("*/**/BUILD.bazel"))