diff --git a/scripts/clean-go-files.ps1 b/scripts/clean-go-files.ps1
index 495dcae83..d1483fe87 100644
--- a/scripts/clean-go-files.ps1
+++ b/scripts/clean-go-files.ps1
@@ -1,4 +1,8 @@
-$directories = Get-ChildItem -Path $env:MainDirectory -Directory -Exclude @("core", "scripts", ".github" , "tests")
+# Only generated model/request-builder directories should be removed before regeneration.
+# Exclude hand-maintained folders and ALL dot-directories (".*" matches .github, .config,
+# .azure-pipelines, .vscode, .devcontainer, etc.) so repo tooling, CI and security-baseline
+# config are not deleted by generation runs.
+$directories = Get-ChildItem -Path $env:MainDirectory -Directory -Exclude @("core", "scripts", "tests", ".*")
 foreach ($directory in $directories) {
 	Remove-Item -Path $directory.FullName -Recurse -Force -Verbose -Exclude *change_notification*, "change_type.go", "lifecycle_event_type.go", "resource_data.go", "resource_permission.go" , "resource_permission_collection_response.go"
 }