diff --git a/clippy.toml b/clippy.toml
index 0f58a29c9..0f77d950b 100644
--- a/clippy.toml
+++ b/clippy.toml
@@ -1,9 +1,16 @@
 disallowed-methods = [
     { path = "rand::thread_rng", reason = "Do not use rand::* directly. Instead, use functions from random.rs" },
-    # We still have `std::fs` references.
-    # { path = "std::fs", reason = "Do not use std::fs directly. Instead, use the FileStorageProvider." },
+    { path = "std::fs::File::create", reason = "Do not use std::fs::File::create directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::File::create_new", reason = "Do not use std::fs::File::create_new directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::OpenOptions::open", reason = "Do not use std::fs::OpenOptions::open for writing. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::write", reason = "Do not use std::fs::write directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::remove_file", reason = "Do not use std::fs::remove_file directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::remove_dir", reason = "Do not use std::fs::remove_dir directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::remove_dir_all", reason = "Do not use std::fs::remove_dir_all directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::create_dir", reason = "Do not use std::fs::create_dir directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
+    { path = "std::fs::create_dir_all", reason = "Do not use std::fs::create_dir_all directly. Use FileStorageProvider in production code or VirtualStorageProvider in tests." },
     { path = "vfs::PhysicalFS::new", reason = "Do not use vfs::PhysicalFS in tests. Instead, use the VirtualStorageProvider::new_overlay()." },
-    { path = "diskann_providers::storage::virtual_storage_provider::VirtualStorageProvider::new_physical", reason = "Do not use VirtualStorageProvider::new_physical() in tests. Instead, use VirtualStorageProvider::new_overlay()." },
+    { path = "diskann_providers::storage::virtual_storage_provider::VirtualStorageProvider::new_physical", reason = "In most tests, use VirtualStorageProvider::new_memory() or new_overlay(). Only use new_physical() for integration tests that require actual filesystem operations (e.g., testing BfTree with its disk backend).", allow-invalid = true },
     # Disallowed methods for the rayon crate to enforce execution within a specified thread pool instead of the global thread pool.
     { path = "rayon::iter::ParallelIterator::for_each", reason = "Use `for_each_in_pool` from rayon_utils.rs instead to enforce execution within a specified thread pool."},
     { path = "rayon::iter::ParallelIterator::for_each_with", reason = "Use `for_each_with_in_pool` instead to enforce execution within a specified thread pool."},
diff --git a/diskann-providers/src/model/graph/provider/async_/bf_tree/provider.rs b/diskann-providers/src/model/graph/provider/async_/bf_tree/provider.rs
index 8650b969f..79388a246 100644
--- a/diskann-providers/src/model/graph/provider/async_/bf_tree/provider.rs
+++ b/diskann-providers/src/model/graph/provider/async_/bf_tree/provider.rs
@@ -2176,7 +2176,6 @@ where
 mod tests {
     use super::*;
     use crate::model::graph::provider::async_::common::TableBasedDeletes;
-    use crate::storage::file_storage_provider::FileStorageProvider;
 
     #[tokio::test]
     async fn test_data_provider_and_delete_interface() {
@@ -2365,6 +2364,7 @@ mod tests {
     // SaveWith/LoadWith Tests for BfTree-based //
     ///////////////////////////////////////////////
 
+    use crate::storage::VirtualStorageProvider;
     use tempfile::tempdir;
 
     /// Test saving and loading of BfTreeProvider without quantization, including deleted vertices
@@ -2453,7 +2453,7 @@ mod tests {
         assert_eq!(vector_config.get_leaf_page_size(), 8192);
         assert_eq!(vector_config.get_cb_max_record_size(), 1024);
 
-        let storage = FileStorageProvider;
+        let storage = VirtualStorageProvider::new_overlay(temp_path);
 
         provider.save_with(&storage, &prefix).await.unwrap();
 
@@ -2621,7 +2621,7 @@ mod tests {
             );
         }
 
-        let storage = FileStorageProvider;
+        let storage = VirtualStorageProvider::new_overlay(temp_path);
 
         provider.save_with(&storage, &prefix).await.unwrap();
 
diff --git a/diskann-providers/src/storage/file_storage_provider.rs b/diskann-providers/src/storage/file_storage_provider.rs
index 9d4d351a4..b0163613b 100644
--- a/diskann-providers/src/storage/file_storage_provider.rs
+++ b/diskann-providers/src/storage/file_storage_provider.rs
@@ -31,6 +31,10 @@ impl StorageReadProvider for FileStorageProvider {
     }
 }
 
+#[expect(
+    clippy::disallowed_methods,
+    reason = "FileStorageProvider is the abstraction layer that wraps std::fs for production use"
+)]
 impl StorageWriteProvider for FileStorageProvider {
     type Writer = BufWriter<File>;
 
@@ -54,6 +58,10 @@ impl StorageWriteProvider for FileStorageProvider {
 }
 
 #[cfg(test)]
+#[expect(
+    clippy::disallowed_methods,
+    reason = "These tests verify FileStorageProvider's functionality with real filesystem operations"
+)]
 mod tests {
     use std::io::{Read, Seek, SeekFrom, Write};
 
diff --git a/diskann-providers/src/storage/mod.rs b/diskann-providers/src/storage/mod.rs
index 1233b11f6..41532851a 100644
--- a/diskann-providers/src/storage/mod.rs
+++ b/diskann-providers/src/storage/mod.rs
@@ -20,7 +20,7 @@ pub(crate) mod bin;
 
 pub(crate) mod file_storage_provider;
 // Use VirtualStorageProvider in tests to avoid filesystem side-effects
-#[cfg(not(test))]
+#[cfg(not(any(test, feature = "testing", feature = "virtual_storage")))]
 pub use file_storage_provider::FileStorageProvider;
 
 mod pq_storage;
diff --git a/diskann-providers/src/utils/generate_synthetic_labels_utils.rs b/diskann-providers/src/utils/generate_synthetic_labels_utils.rs
index 38720914c..5f26e0b97 100644
--- a/diskann-providers/src/utils/generate_synthetic_labels_utils.rs
+++ b/diskann-providers/src/utils/generate_synthetic_labels_utils.rs
@@ -80,6 +80,10 @@ impl ZipfDistribution {
     }
 }
 
+#[expect(
+    clippy::disallowed_methods,
+    reason = "Utility function for generating synthetic label files, needs direct file creation"
+)]
 pub fn generate_labels(
     output_file: &str,
     distribution_type: &str,
@@ -128,6 +132,10 @@ pub fn generate_labels(
 }
 
 #[cfg(test)]
+#[expect(
+    clippy::disallowed_methods,
+    reason = "Test for generate_labels function which creates files, needs cleanup with fs::remove_file"
+)]
 mod test {
     use std::fs;