diff --git a/Cargo.lock b/Cargo.lock
index af6cb8c8da..b4fe23b69f 100644
--- a/Cargo.lock
+++ b/Cargo.lock
@@ -2724,7 +2724,7 @@ checksum = "e86697c916019a8588c99b5fac3cead74ec0b4b819707a682fd4d23fa0ce1ba1"
 [[package]]
 name = "salsa"
 version = "0.18.0"
-source = "git+https://github.com/salsa-rs/salsa.git?rev=cd339fc1c9a6ea0ffb1d09bd3bffb5633f776ef3#cd339fc1c9a6ea0ffb1d09bd3bffb5633f776ef3"
+source = "git+https://github.com/MichaReiser/salsa.git?rev=0cae5c52a3240172ef0be5c9d19e63448c53397c#0cae5c52a3240172ef0be5c9d19e63448c53397c"
 dependencies = [
  "arc-swap",
  "boomphf",
@@ -2744,12 +2744,12 @@ dependencies = [
 [[package]]
 name = "salsa-macro-rules"
 version = "0.1.0"
-source = "git+https://github.com/salsa-rs/salsa.git?rev=cd339fc1c9a6ea0ffb1d09bd3bffb5633f776ef3#cd339fc1c9a6ea0ffb1d09bd3bffb5633f776ef3"
+source = "git+https://github.com/MichaReiser/salsa.git?rev=0cae5c52a3240172ef0be5c9d19e63448c53397c#0cae5c52a3240172ef0be5c9d19e63448c53397c"
 
 [[package]]
 name = "salsa-macros"
 version = "0.18.0"
-source = "git+https://github.com/salsa-rs/salsa.git?rev=cd339fc1c9a6ea0ffb1d09bd3bffb5633f776ef3#cd339fc1c9a6ea0ffb1d09bd3bffb5633f776ef3"
+source = "git+https://github.com/MichaReiser/salsa.git?rev=0cae5c52a3240172ef0be5c9d19e63448c53397c#0cae5c52a3240172ef0be5c9d19e63448c53397c"
 dependencies = [
  "heck",
  "proc-macro2",
diff --git a/Cargo.toml b/Cargo.toml
index 05646a919d..77e326a4c6 100644
--- a/Cargo.toml
+++ b/Cargo.toml
@@ -107,7 +107,7 @@ rand = { version = "0.8.5" }
 rayon = { version = "1.10.0" }
 regex = { version = "1.10.2" }
 rustc-hash = { version = "2.0.0" }
-salsa = { git = "https://github.com/salsa-rs/salsa.git", rev = "cd339fc1c9a6ea0ffb1d09bd3bffb5633f776ef3" }
+salsa = { git = "https://github.com/MichaReiser/salsa.git", rev = "0cae5c52a3240172ef0be5c9d19e63448c53397c" }
 schemars = { version = "0.8.16" }
 seahash = { version = "4.1.0" }
 serde = { version = "1.0.197", features = ["derive"] }
diff --git a/crates/red_knot/src/db/changes.rs b/crates/red_knot/src/db/changes.rs
index df527f68fd..d97cc4f034 100644
--- a/crates/red_knot/src/db/changes.rs
+++ b/crates/red_knot/src/db/changes.rs
@@ -173,7 +173,7 @@ impl RootDatabase {
                 let package = workspace.package(self, &path);
                 let file = system_path_to_file(self, &path);
 
-                if let (Some(package), Some(file)) = (package, file) {
+                if let (Some(package), Ok(file)) = (package, file) {
                     package.add_file(self, file);
                 }
             }
diff --git a/crates/red_knot/src/workspace.rs b/crates/red_knot/src/workspace.rs
index 5ab8e89f80..d262ef39b0 100644
--- a/crates/red_knot/src/workspace.rs
+++ b/crates/red_knot/src/workspace.rs
@@ -1,4 +1,4 @@
-use salsa::Setter as _;
+use salsa::{Durability, Setter as _};
 use std::{collections::BTreeMap, sync::Arc};
 
 use rustc_hash::{FxBuildHasher, FxHashSet};
@@ -105,7 +105,9 @@ impl Workspace {
             packages.insert(package.root.clone(), Package::from_metadata(db, package));
         }
 
-        Workspace::new(db, metadata.root, None, packages)
+        Workspace::builder(metadata.root, None, packages)
+            .durability(Durability::MEDIUM)
+            .new(db)
     }
 
     pub fn root(self, db: &dyn Db) -> &SystemPath {
@@ -136,7 +138,9 @@ impl Workspace {
             new_packages.insert(path, package);
         }
 
-        self.set_package_tree(db).to(new_packages);
+        self.set_package_tree(db)
+            .with_durability(Durability::MEDIUM)
+            .to(new_packages);
     }
 
     #[tracing::instrument(level = "debug", skip_all)]
@@ -305,20 +309,28 @@ impl Package {
     }
 
     fn from_metadata(db: &dyn Db, metadata: PackageMetadata) -> Self {
-        Self::new(db, metadata.name, metadata.root, PackageFiles::default())
+        Self::builder(metadata.name, metadata.root, PackageFiles::default())
+            .durability(Durability::MEDIUM)
+            .new(db)
     }
 
     fn update(self, db: &mut dyn Db, metadata: PackageMetadata) {
         let root = self.root(db);
         assert_eq!(root, metadata.root());
 
-        self.set_name(db).to(metadata.name);
+        if self.name(db) != metadata.name() {
+            self.set_name(db)
+                .with_durability(Durability::MEDIUM)
+                .to(metadata.name);
+        }
     }
 
     #[tracing::instrument(level = "debug", skip(db))]
     pub fn reload_files(self, db: &mut dyn Db) {
-        // Force a re-index of the files in the next revision.
-        self.set_file_set(db).to(PackageFiles::lazy());
+        if !self.file_set(db).is_lazy() {
+            // Force a re-index of the files in the next revision.
+            self.set_file_set(db).to(PackageFiles::lazy());
+        }
     }
 }
 
@@ -364,7 +376,7 @@ fn discover_package_files(db: &dyn Db, path: &SystemPath) -> FxHashSet<File> {
     for path in paths {
         // If this returns `None`, then the file was deleted between the `walk_directory` call and now.
         // We can ignore this.
-        if let Some(file) = system_path_to_file(db.upcast(), &path) {
+        if let Ok(file) = system_path_to_file(db.upcast(), &path) {
             files.insert(file);
         }
     }
diff --git a/crates/red_knot/src/workspace/files.rs b/crates/red_knot/src/workspace/files.rs
index ab5c0fb868..ae391fdcd2 100644
--- a/crates/red_knot/src/workspace/files.rs
+++ b/crates/red_knot/src/workspace/files.rs
@@ -47,6 +47,10 @@ impl PackageFiles {
         }
     }
 
+    pub fn is_lazy(&self) -> bool {
+        matches!(*self.state.lock().unwrap(), State::Lazy)
+    }
+
     /// Returns a mutable view on the index that allows cheap in-place mutations.
     ///
     /// The changes are automatically written back to the database once the view is dropped.
diff --git a/crates/red_knot/tests/file_watching.rs b/crates/red_knot/tests/file_watching.rs
index 915a4182ad..9af46cf73c 100644
--- a/crates/red_knot/tests/file_watching.rs
+++ b/crates/red_knot/tests/file_watching.rs
@@ -10,7 +10,7 @@ use red_knot::watch;
 use red_knot::watch::{directory_watcher, WorkspaceWatcher};
 use red_knot::workspace::WorkspaceMetadata;
 use red_knot_module_resolver::{resolve_module, ModuleName};
-use ruff_db::files::{system_path_to_file, File};
+use ruff_db::files::{system_path_to_file, File, FileError};
 use ruff_db::program::{Program, ProgramSettings, SearchPathSettings, TargetVersion};
 use ruff_db::source::source_text;
 use ruff_db::system::{OsSystem, SystemPath, SystemPathBuf};
@@ -82,7 +82,7 @@ impl TestCase {
         collected
     }
 
-    fn system_file(&self, path: impl AsRef<SystemPath>) -> Option<File> {
+    fn system_file(&self, path: impl AsRef<SystemPath>) -> Result<File, FileError> {
         system_path_to_file(self.db(), path.as_ref())
     }
 }
@@ -190,7 +190,7 @@ fn new_file() -> anyhow::Result<()> {
     let bar_file = case.system_file(&bar_path).unwrap();
     let foo_path = case.workspace_path("foo.py");
 
-    assert_eq!(case.system_file(&foo_path), None);
+    assert_eq!(case.system_file(&foo_path), Err(FileError::NotFound));
     assert_eq!(&case.collect_package_files(&bar_path), &[bar_file]);
 
     std::fs::write(foo_path.as_std_path(), "print('Hello')")?;
@@ -213,7 +213,7 @@ fn new_ignored_file() -> anyhow::Result<()> {
     let bar_file = case.system_file(&bar_path).unwrap();
     let foo_path = case.workspace_path("foo.py");
 
-    assert_eq!(case.system_file(&foo_path), None);
+    assert_eq!(case.system_file(&foo_path), Err(FileError::NotFound));
     assert_eq!(&case.collect_package_files(&bar_path), &[bar_file]);
 
     std::fs::write(foo_path.as_std_path(), "print('Hello')")?;
@@ -222,7 +222,7 @@ fn new_ignored_file() -> anyhow::Result<()> {
 
     case.db_mut().apply_changes(changes);
 
-    assert!(case.system_file(&foo_path).is_some());
+    assert!(case.system_file(&foo_path).is_ok());
     assert_eq!(&case.collect_package_files(&bar_path), &[bar_file]);
 
     Ok(())
@@ -234,9 +234,7 @@ fn changed_file() -> anyhow::Result<()> {
     let mut case = setup([("foo.py", foo_source)])?;
     let foo_path = case.workspace_path("foo.py");
 
-    let foo = case
-        .system_file(&foo_path)
-        .ok_or_else(|| anyhow!("Foo not found"))?;
+    let foo = case.system_file(&foo_path)?;
     assert_eq!(source_text(case.db(), foo).as_str(), foo_source);
     assert_eq!(&case.collect_package_files(&foo_path), &[foo]);
 
@@ -260,9 +258,7 @@ fn changed_metadata() -> anyhow::Result<()> {
     let mut case = setup([("foo.py", "")])?;
     let foo_path = case.workspace_path("foo.py");
 
-    let foo = case
-        .system_file(&foo_path)
-        .ok_or_else(|| anyhow!("Foo not found"))?;
+    let foo = case.system_file(&foo_path)?;
     assert_eq!(
         foo.permissions(case.db()),
         Some(
@@ -302,9 +298,7 @@ fn deleted_file() -> anyhow::Result<()> {
     let mut case = setup([("foo.py", foo_source)])?;
     let foo_path = case.workspace_path("foo.py");
 
-    let foo = case
-        .system_file(&foo_path)
-        .ok_or_else(|| anyhow!("Foo not found"))?;
+    let foo = case.system_file(&foo_path)?;
 
     assert!(foo.exists(case.db()));
     assert_eq!(&case.collect_package_files(&foo_path), &[foo]);
@@ -333,9 +327,7 @@ fn move_file_to_trash() -> anyhow::Result<()> {
     let trash_path = case.root_path().join(".trash");
     std::fs::create_dir_all(trash_path.as_std_path())?;
 
-    let foo = case
-        .system_file(&foo_path)
-        .ok_or_else(|| anyhow!("Foo not found"))?;
+    let foo = case.system_file(&foo_path)?;
 
     assert!(foo.exists(case.db()));
     assert_eq!(&case.collect_package_files(&foo_path), &[foo]);
@@ -367,7 +359,7 @@ fn move_file_to_workspace() -> anyhow::Result<()> {
 
     let foo_in_workspace_path = case.workspace_path("foo.py");
 
-    assert!(case.system_file(&foo_path).is_some());
+    assert!(case.system_file(&foo_path).is_ok());
     assert_eq!(&case.collect_package_files(&bar_path), &[bar]);
     assert!(case
         .db()
@@ -381,9 +373,7 @@ fn move_file_to_workspace() -> anyhow::Result<()> {
 
     case.db_mut().apply_changes(changes);
 
-    let foo_in_workspace = case
-        .system_file(&foo_in_workspace_path)
-        .ok_or_else(|| anyhow!("Foo not found"))?;
+    let foo_in_workspace = case.system_file(&foo_in_workspace_path)?;
 
     assert!(foo_in_workspace.exists(case.db()));
     assert_eq!(
@@ -401,9 +391,7 @@ fn rename_file() -> anyhow::Result<()> {
     let foo_path = case.workspace_path("foo.py");
     let bar_path = case.workspace_path("bar.py");
 
-    let foo = case
-        .system_file(&foo_path)
-        .ok_or_else(|| anyhow!("Foo not found"))?;
+    let foo = case.system_file(&foo_path)?;
 
     assert_eq!(case.collect_package_files(&foo_path), [foo]);
 
@@ -415,9 +403,7 @@ fn rename_file() -> anyhow::Result<()> {
 
     assert!(!foo.exists(case.db()));
 
-    let bar = case
-        .system_file(&bar_path)
-        .ok_or_else(|| anyhow!("Bar not found"))?;
+    let bar = case.system_file(&bar_path)?;
 
     assert!(bar.exists(case.db()));
     assert_eq!(case.collect_package_files(&foo_path), [bar]);
diff --git a/crates/red_knot_module_resolver/src/path.rs b/crates/red_knot_module_resolver/src/path.rs
index e9fdcd493d..eea4948b48 100644
--- a/crates/red_knot_module_resolver/src/path.rs
+++ b/crates/red_knot_module_resolver/src/path.rs
@@ -5,7 +5,7 @@ use std::sync::Arc;
 
 use camino::{Utf8Path, Utf8PathBuf};
 
-use ruff_db::files::{system_path_to_file, vendored_path_to_file, File};
+use ruff_db::files::{system_path_to_file, vendored_path_to_file, File, FileError};
 use ruff_db::system::{System, SystemPath, SystemPathBuf};
 use ruff_db::vendored::{VendoredPath, VendoredPathBuf};
 
@@ -68,16 +68,18 @@ impl ModulePath {
             SearchPathInner::Extra(search_path)
             | SearchPathInner::FirstParty(search_path)
             | SearchPathInner::SitePackages(search_path)
-            | SearchPathInner::Editable(search_path) => resolver
-                .system()
-                .is_directory(&search_path.join(relative_path)),
+            | SearchPathInner::Editable(search_path) => {
+                system_path_to_file(resolver.db.upcast(), search_path.join(relative_path))
+                    == Err(FileError::IsADirectory)
+            }
             SearchPathInner::StandardLibraryCustom(stdlib_root) => {
                 match query_stdlib_version(Some(stdlib_root), relative_path, resolver) {
                     TypeshedVersionsQueryResult::DoesNotExist => false,
                     TypeshedVersionsQueryResult::Exists
-                    | TypeshedVersionsQueryResult::MaybeExists => resolver
-                        .system()
-                        .is_directory(&stdlib_root.join(relative_path)),
+                    | TypeshedVersionsQueryResult::MaybeExists => {
+                        system_path_to_file(resolver.db.upcast(), stdlib_root.join(relative_path))
+                            == Err(FileError::IsADirectory)
+                    }
                 }
             }
             SearchPathInner::StandardLibraryVendored(stdlib_root) => {
@@ -105,10 +107,9 @@ impl ModulePath {
             | SearchPathInner::SitePackages(search_path)
             | SearchPathInner::Editable(search_path) => {
                 let absolute_path = search_path.join(relative_path);
-                system_path_to_file(resolver.db.upcast(), absolute_path.join("__init__.py"))
-                    .is_some()
+                system_path_to_file(resolver.db.upcast(), absolute_path.join("__init__.py")).is_ok()
                     || system_path_to_file(resolver.db.upcast(), absolute_path.join("__init__.py"))
-                        .is_some()
+                        .is_ok()
             }
             SearchPathInner::StandardLibraryCustom(search_path) => {
                 match query_stdlib_version(Some(search_path), relative_path, resolver) {
@@ -118,7 +119,7 @@ impl ModulePath {
                         resolver.db.upcast(),
                         search_path.join(relative_path).join("__init__.pyi"),
                     )
-                    .is_some(),
+                    .is_ok(),
                 }
             }
             SearchPathInner::StandardLibraryVendored(search_path) => {
@@ -145,14 +146,14 @@ impl ModulePath {
             | SearchPathInner::FirstParty(search_path)
             | SearchPathInner::SitePackages(search_path)
             | SearchPathInner::Editable(search_path) => {
-                system_path_to_file(db, search_path.join(relative_path))
+                system_path_to_file(db, search_path.join(relative_path)).ok()
             }
             SearchPathInner::StandardLibraryCustom(stdlib_root) => {
                 match query_stdlib_version(Some(stdlib_root), relative_path, resolver) {
                     TypeshedVersionsQueryResult::DoesNotExist => None,
                     TypeshedVersionsQueryResult::Exists
                     | TypeshedVersionsQueryResult::MaybeExists => {
-                        system_path_to_file(db, stdlib_root.join(relative_path))
+                        system_path_to_file(db, stdlib_root.join(relative_path)).ok()
                     }
                 }
             }
@@ -161,7 +162,7 @@ impl ModulePath {
                     TypeshedVersionsQueryResult::DoesNotExist => None,
                     TypeshedVersionsQueryResult::Exists
                     | TypeshedVersionsQueryResult::MaybeExists => {
-                        vendored_path_to_file(db, stdlib_root.join(relative_path))
+                        vendored_path_to_file(db, stdlib_root.join(relative_path)).ok()
                     }
                 }
             }
@@ -301,11 +302,15 @@ pub(crate) enum SearchPathValidationError {
     /// (This is only relevant for stdlib search paths.)
     NoStdlibSubdirectory(SystemPathBuf),
 
-    /// The path provided by the user is a directory,
+    /// The typeshed path provided by the user is a directory,
     /// but no `stdlib/VERSIONS` file exists.
     /// (This is only relevant for stdlib search paths.)
     NoVersionsFile(SystemPathBuf),
 
+    /// `stdlib/VERSIONS` is a directory.
+    /// (This is only relevant for stdlib search paths.)
+    VersionsIsADirectory(SystemPathBuf),
+
     /// The path provided by the user is a directory,
     /// and a `stdlib/VERSIONS` file exists, but it fails to parse.
     /// (This is only relevant for stdlib search paths.)
@@ -320,6 +325,7 @@ impl fmt::Display for SearchPathValidationError {
                 write!(f, "The directory at {path} has no `stdlib/` subdirectory")
             }
             Self::NoVersionsFile(path) => write!(f, "Expected a file at {path}/stldib/VERSIONS"),
+            Self::VersionsIsADirectory(path) => write!(f, "{path}/stldib/VERSIONS is a directory."),
             Self::VersionsParseError(underlying_error) => underlying_error.fmt(f),
         }
     }
@@ -408,10 +414,13 @@ impl SearchPath {
                 typeshed.to_path_buf(),
             ));
         }
-        let Some(typeshed_versions) = system_path_to_file(db.upcast(), stdlib.join("VERSIONS"))
-        else {
-            return Err(SearchPathValidationError::NoVersionsFile(typeshed));
-        };
+        let typeshed_versions =
+            system_path_to_file(db.upcast(), stdlib.join("VERSIONS")).map_err(|err| match err {
+                FileError::NotFound => SearchPathValidationError::NoVersionsFile(typeshed),
+                FileError::IsADirectory => {
+                    SearchPathValidationError::VersionsIsADirectory(typeshed)
+                }
+            })?;
         crate::typeshed::parse_typeshed_versions(db, typeshed_versions)
             .as_ref()
             .map_err(|validation_error| {
diff --git a/crates/red_knot_module_resolver/src/resolver.rs b/crates/red_knot_module_resolver/src/resolver.rs
index ff8165b22c..8587cbe819 100644
--- a/crates/red_knot_module_resolver/src/resolver.rs
+++ b/crates/red_knot_module_resolver/src/resolver.rs
@@ -489,6 +489,7 @@ fn resolve_name(db: &dyn Db, name: &ModuleName) -> Option<(SearchPath, File, Mod
         if is_builtin_module && !search_path.is_standard_library() {
             continue;
         }
+
         let mut components = name.components();
         let module_name = components.next_back()?;
 
@@ -1282,6 +1283,7 @@ mod tests {
         db.memory_file_system()
             .remove_directory(foo_init_path.parent().unwrap())?;
         File::sync_path(&mut db, &foo_init_path);
+        File::sync_path(&mut db, foo_init_path.parent().unwrap());
 
         let foo_module = resolve_module(&db, foo_module_name).expect("Foo module to resolve");
         assert_eq!(&src.join("foo.py"), foo_module.file().path(&db));
@@ -1312,7 +1314,7 @@ mod tests {
         let functools_module = resolve_module(&db, functools_module_name.clone()).unwrap();
         assert_eq!(functools_module.search_path(), &stdlib);
         assert_eq!(
-            Some(functools_module.file()),
+            Ok(functools_module.file()),
             system_path_to_file(&db, &stdlib_functools_path)
         );
 
@@ -1332,7 +1334,7 @@ mod tests {
         );
         assert_eq!(functools_module.search_path(), &stdlib);
         assert_eq!(
-            Some(functools_module.file()),
+            Ok(functools_module.file()),
             system_path_to_file(&db, &stdlib_functools_path)
         );
     }
@@ -1358,7 +1360,7 @@ mod tests {
         let functools_module = resolve_module(&db, functools_module_name.clone()).unwrap();
         assert_eq!(functools_module.search_path(), &stdlib);
         assert_eq!(
-            Some(functools_module.file()),
+            Ok(functools_module.file()),
             system_path_to_file(&db, stdlib.join("functools.pyi"))
         );
 
@@ -1369,7 +1371,7 @@ mod tests {
         let functools_module = resolve_module(&db, functools_module_name.clone()).unwrap();
         assert_eq!(functools_module.search_path(), &src);
         assert_eq!(
-            Some(functools_module.file()),
+            Ok(functools_module.file()),
             system_path_to_file(&db, &src_functools_path)
         );
     }
@@ -1400,7 +1402,7 @@ mod tests {
         let functools_module = resolve_module(&db, functools_module_name.clone()).unwrap();
         assert_eq!(functools_module.search_path(), &src);
         assert_eq!(
-            Some(functools_module.file()),
+            Ok(functools_module.file()),
             system_path_to_file(&db, &src_functools_path)
         );
 
@@ -1413,7 +1415,7 @@ mod tests {
         let functools_module = resolve_module(&db, functools_module_name.clone()).unwrap();
         assert_eq!(functools_module.search_path(), &stdlib);
         assert_eq!(
-            Some(functools_module.file()),
+            Ok(functools_module.file()),
             system_path_to_file(&db, stdlib.join("functools.pyi"))
         );
     }
diff --git a/crates/red_knot_module_resolver/src/state.rs b/crates/red_knot_module_resolver/src/state.rs
index 048504f60c..ec32c3e791 100644
--- a/crates/red_knot_module_resolver/src/state.rs
+++ b/crates/red_knot_module_resolver/src/state.rs
@@ -1,5 +1,4 @@
 use ruff_db::program::TargetVersion;
-use ruff_db::system::System;
 use ruff_db::vendored::VendoredFileSystem;
 
 use crate::db::Db;
@@ -20,10 +19,6 @@ impl<'db> ResolverState<'db> {
         }
     }
 
-    pub(crate) fn system(&self) -> &dyn System {
-        self.db.system()
-    }
-
     pub(crate) fn vendored(&self) -> &VendoredFileSystem {
         self.db.vendored()
     }
diff --git a/crates/red_knot_module_resolver/src/typeshed/versions.rs b/crates/red_knot_module_resolver/src/typeshed/versions.rs
index d0aef6e0bd..e5aae22c5f 100644
--- a/crates/red_knot_module_resolver/src/typeshed/versions.rs
+++ b/crates/red_knot_module_resolver/src/typeshed/versions.rs
@@ -52,7 +52,7 @@ impl<'db> LazyTypeshedVersions<'db> {
             } else {
                 return &VENDORED_VERSIONS;
             };
-            let Some(versions_file) = system_path_to_file(db.upcast(), &versions_path) else {
+            let Ok(versions_file) = system_path_to_file(db.upcast(), &versions_path) else {
                 todo!(
                     "Still need to figure out how to handle VERSIONS files being deleted \
                     from custom typeshed directories! Expected a file to exist at {versions_path}"
diff --git a/crates/ruff_db/src/files.rs b/crates/ruff_db/src/files.rs
index 88c768c7eb..2ad371542b 100644
--- a/crates/ruff_db/src/files.rs
+++ b/crates/ruff_db/src/files.rs
@@ -1,8 +1,9 @@
+use std::fmt::Formatter;
 use std::sync::Arc;
 
 use countme::Count;
 use dashmap::mapref::entry::Entry;
-use salsa::Setter;
+use salsa::{Durability, Setter};
 
 pub use file_root::{FileRoot, FileRootKind};
 pub use path::FilePath;
@@ -13,28 +14,35 @@ use crate::files::file_root::FileRoots;
 use crate::files::private::FileStatus;
 use crate::system::{Metadata, SystemPath, SystemPathBuf, SystemVirtualPath, SystemVirtualPathBuf};
 use crate::vendored::{VendoredPath, VendoredPathBuf};
-use crate::{Db, FxDashMap};
+use crate::{vendored, Db, FxDashMap};
 
 mod file_root;
 mod path;
 
 /// Interns a file system path and returns a salsa `File` ingredient.
 ///
-/// Returns `None` if the path doesn't exist, isn't accessible, or if the path points to a directory.
+/// Returns `Err` if the path doesn't exist, isn't accessible, or if the path points to a directory.
 #[inline]
-pub fn system_path_to_file(db: &dyn Db, path: impl AsRef<SystemPath>) -> Option<File> {
+pub fn system_path_to_file(db: &dyn Db, path: impl AsRef<SystemPath>) -> Result<File, FileError> {
     let file = db.files().system(db, path.as_ref());
 
     // It's important that `vfs.file_system` creates a `VfsFile` even for files that don't exist or don't
     // exist anymore so that Salsa can track that the caller of this function depends on the existence of
     // that file. This function filters out files that don't exist, but Salsa will know that it must
     // re-run the calling query whenever the `file`'s status changes (because of the `.status` call here).
-    file.exists(db).then_some(file)
+    match file.status(db) {
+        FileStatus::Exists => Ok(file),
+        FileStatus::IsADirectory => Err(FileError::IsADirectory),
+        FileStatus::NotFound => Err(FileError::NotFound),
+    }
 }
 
 /// Interns a vendored file path. Returns `Some` if the vendored file for `path` exists and `None` otherwise.
 #[inline]
-pub fn vendored_path_to_file(db: &dyn Db, path: impl AsRef<VendoredPath>) -> Option<File> {
+pub fn vendored_path_to_file(
+    db: &dyn Db,
+    path: impl AsRef<VendoredPath>,
+) -> Result<File, FileError> {
     db.files().vendored(db, path.as_ref())
 }
 
@@ -68,7 +76,7 @@ impl Files {
     /// For a non-existing file, creates a new salsa [`File`] ingredient and stores it for future lookups.
     ///
     /// The operation always succeeds even if the path doesn't exist on disk, isn't accessible or if the path points to a directory.
-    /// In these cases, a file with status [`FileStatus::Deleted`] is returned.
+    /// In these cases, a file with status [`FileStatus::NotFound`] is returned.
     #[tracing::instrument(level = "trace", skip(self, db))]
     fn system(&self, db: &dyn Db, path: &SystemPath) -> File {
         let absolute = SystemPath::absolute(path, db.system().current_directory());
@@ -78,27 +86,32 @@ impl Files {
             .system_by_path
             .entry(absolute.clone())
             .or_insert_with(|| {
-                // TODO: Set correct durability according to source root.
                 let metadata = db.system().path_metadata(path);
+                let durability = self
+                    .root(db, path)
+                    .map_or(Durability::default(), |root| root.durability(db));
 
-                match metadata {
-                    Ok(metadata) if metadata.file_type().is_file() => File::new(
-                        db,
-                        FilePath::System(absolute),
+                let (permissions, revision, status) = match metadata {
+                    Ok(metadata) if metadata.file_type().is_file() => (
                         metadata.permissions(),
                         metadata.revision(),
                         FileStatus::Exists,
-                        Count::default(),
                     ),
-                    _ => File::new(
-                        db,
-                        FilePath::System(absolute),
-                        None,
-                        FileRevision::zero(),
-                        FileStatus::Deleted,
-                        Count::default(),
-                    ),
-                }
+                    Ok(metadata) if metadata.file_type().is_directory() => {
+                        (None, FileRevision::zero(), FileStatus::IsADirectory)
+                    }
+                    _ => (None, FileRevision::zero(), FileStatus::NotFound),
+                };
+
+                File::builder(
+                    FilePath::System(absolute),
+                    permissions,
+                    revision,
+                    status,
+                    Count::default(),
+                )
+                .durability(durability)
+                .new(db)
             })
     }
 
@@ -114,20 +127,27 @@ impl Files {
     /// Looks up a vendored file by its path. Returns `Some` if a vendored file for the given path
     /// exists and `None` otherwise.
     #[tracing::instrument(level = "trace", skip(self, db))]
-    fn vendored(&self, db: &dyn Db, path: &VendoredPath) -> Option<File> {
+    fn vendored(&self, db: &dyn Db, path: &VendoredPath) -> Result<File, FileError> {
         let file = match self.inner.vendored_by_path.entry(path.to_path_buf()) {
             Entry::Occupied(entry) => *entry.get(),
             Entry::Vacant(entry) => {
-                let metadata = db.vendored().metadata(path).ok()?;
+                let metadata = match db.vendored().metadata(path) {
+                    Ok(metadata) => match metadata.kind() {
+                        vendored::FileType::File => metadata,
+                        vendored::FileType::Directory => return Err(FileError::IsADirectory),
+                    },
+                    Err(_) => return Err(FileError::NotFound),
+                };
 
-                let file = File::new(
-                    db,
+                let file = File::builder(
                     FilePath::Vendored(path.to_path_buf()),
                     Some(0o444),
                     metadata.revision(),
                     FileStatus::Exists,
                     Count::default(),
-                );
+                )
+                .durability(Durability::HIGH)
+                .new(db);
 
                 entry.insert(file);
 
@@ -135,7 +155,7 @@ impl Files {
             }
         };
 
-        Some(file)
+        Ok(file)
     }
 
     /// Looks up a virtual file by its `path`.
@@ -210,8 +230,7 @@ impl Files {
         let inner = Arc::clone(&db.files().inner);
         for entry in inner.system_by_path.iter_mut() {
             if entry.key().starts_with(&path) {
-                let file = entry.value();
-                file.sync(db);
+                File::sync_system_path(db, entry.key(), Some(*entry.value()));
             }
         }
 
@@ -219,7 +238,9 @@ impl Files {
 
         for root in roots.all() {
             if root.path(db).starts_with(&path) {
-                root.set_revision(db).to(FileRevision::now());
+                root.set_revision(db)
+                    .with_durability(Durability::HIGH)
+                    .to(FileRevision::now());
             }
         }
     }
@@ -236,14 +257,15 @@ impl Files {
     pub fn sync_all(db: &mut dyn Db) {
         let inner = Arc::clone(&db.files().inner);
         for entry in inner.system_by_path.iter_mut() {
-            let file = entry.value();
-            file.sync(db);
+            File::sync_system_path(db, entry.key(), Some(*entry.value()));
         }
 
         let roots = inner.roots.read().unwrap();
 
         for root in roots.all() {
-            root.set_revision(db).to(FileRevision::now());
+            root.set_revision(db)
+                .with_durability(Durability::HIGH)
+                .to(FileRevision::now());
         }
     }
 }
@@ -335,6 +357,7 @@ impl File {
     #[tracing::instrument(level = "debug", skip(db))]
     pub fn sync_path(db: &mut dyn Db, path: &SystemPath) {
         let absolute = SystemPath::absolute(path, db.system().current_directory());
+        Files::touch_root(db, &absolute);
         Self::sync_system_path(db, &absolute, None);
     }
 
@@ -345,6 +368,7 @@ impl File {
 
         match path {
             FilePath::System(system) => {
+                Files::touch_root(db, &system);
                 Self::sync_system_path(db, &system, Some(self));
             }
             FilePath::Vendored(_) => {
@@ -357,34 +381,56 @@ impl File {
     }
 
     fn sync_system_path(db: &mut dyn Db, path: &SystemPath, file: Option<File>) {
-        Files::touch_root(db, path);
         let Some(file) = file.or_else(|| db.files().try_system(db, path)) else {
             return;
         };
         let metadata = db.system().path_metadata(path);
-        Self::sync_impl(db, metadata, file);
+        let durability = db.files().root(db, path).map(|root| root.durability(db));
+        Self::sync_impl(db, metadata, file, durability);
     }
 
     fn sync_system_virtual_path(db: &mut dyn Db, path: &SystemVirtualPath, file: File) {
         let metadata = db.system().virtual_path_metadata(path);
-        Self::sync_impl(db, metadata, file);
+        Self::sync_impl(db, metadata, file, None);
     }
 
     /// Private method providing the implementation for [`Self::sync_system_path`] and
     /// [`Self::sync_system_virtual_path`].
-    fn sync_impl(db: &mut dyn Db, metadata: crate::system::Result<Metadata>, file: File) {
+    fn sync_impl(
+        db: &mut dyn Db,
+        metadata: crate::system::Result<Metadata>,
+        file: File,
+        durability: Option<Durability>,
+    ) {
         let (status, revision, permission) = match metadata {
             Ok(metadata) if metadata.file_type().is_file() => (
                 FileStatus::Exists,
                 metadata.revision(),
                 metadata.permissions(),
             ),
-            _ => (FileStatus::Deleted, FileRevision::zero(), None),
+            Ok(metadata) if metadata.file_type().is_directory() => {
+                (FileStatus::IsADirectory, FileRevision::zero(), None)
+            }
+            _ => (FileStatus::NotFound, FileRevision::zero(), None),
         };
 
-        file.set_status(db).to(status);
-        file.set_revision(db).to(revision);
-        file.set_permissions(db).to(permission);
+        let durability = durability.unwrap_or_default();
+
+        if file.status(db) != status {
+            file.set_status(db).with_durability(durability).to(status);
+        }
+
+        if file.revision(db) != revision {
+            file.set_revision(db)
+                .with_durability(durability)
+                .to(revision);
+        }
+
+        if file.permissions(db) != permission {
+            file.set_permissions(db)
+                .with_durability(durability)
+                .to(permission);
+        }
     }
 
     /// Returns `true` if the file exists.
@@ -401,15 +447,35 @@ mod private {
         /// The file exists.
         Exists,
 
-        /// The file was deleted, didn't exist to begin with or the path isn't a file.
-        Deleted,
+        /// The path isn't a file and instead points to a directory.
+        IsADirectory,
+
+        /// The path doesn't exist, isn't accessible, or no longer exists.
+        NotFound,
     }
 }
 
+#[derive(Copy, Clone, Debug, Eq, PartialEq)]
+pub enum FileError {
+    IsADirectory,
+    NotFound,
+}
+
+impl std::fmt::Display for FileError {
+    fn fmt(&self, f: &mut Formatter<'_>) -> std::fmt::Result {
+        match self {
+            FileError::IsADirectory => f.write_str("Is a directory"),
+            FileError::NotFound => f.write_str("Not found"),
+        }
+    }
+}
+
+impl std::error::Error for FileError {}
+
 #[cfg(test)]
 mod tests {
     use crate::file_revision::FileRevision;
-    use crate::files::{system_path_to_file, vendored_path_to_file};
+    use crate::files::{system_path_to_file, vendored_path_to_file, FileError};
     use crate::system::DbWithTestSystem;
     use crate::tests::TestDb;
     use crate::vendored::tests::VendoredFileSystemBuilder;
@@ -435,7 +501,7 @@ mod tests {
 
         let test = system_path_to_file(&db, "test.py");
 
-        assert_eq!(test, None);
+        assert_eq!(test, Err(FileError::NotFound));
     }
 
     #[test]
@@ -477,6 +543,9 @@ mod tests {
     fn stubbed_vendored_file_non_existing() {
         let db = TestDb::new();
 
-        assert_eq!(vendored_path_to_file(&db, "test.py"), None);
+        assert_eq!(
+            vendored_path_to_file(&db, "test.py"),
+            Err(FileError::NotFound)
+        );
     }
 }
diff --git a/crates/ruff_db/src/files/file_root.rs b/crates/ruff_db/src/files/file_root.rs
index 3eb64609b6..6375655edd 100644
--- a/crates/ruff_db/src/files/file_root.rs
+++ b/crates/ruff_db/src/files/file_root.rs
@@ -1,6 +1,7 @@
 use std::fmt::Formatter;
 
 use path_slash::PathExt;
+use salsa::Durability;
 
 use crate::file_revision::FileRevision;
 use crate::system::{SystemPath, SystemPathBuf};
@@ -83,7 +84,9 @@ impl FileRoots {
         let mut route = normalized_path.replace('{', "{{").replace('}', "}}");
 
         // Insert a new source root
-        let root = FileRoot::new(db, path, kind, FileRevision::now());
+        let root = FileRoot::builder(path, kind, FileRevision::now())
+            .durability(Durability::HIGH)
+            .new(db);
 
         // Insert a path that matches the root itself
         self.by_path.insert(route.clone(), root).unwrap();
diff --git a/crates/ruff_db/src/files/path.rs b/crates/ruff_db/src/files/path.rs
index a1c3530ab0..816eaf461a 100644
--- a/crates/ruff_db/src/files/path.rs
+++ b/crates/ruff_db/src/files/path.rs
@@ -95,8 +95,8 @@ impl FilePath {
     #[inline]
     pub fn to_file(&self, db: &dyn Db) -> Option<File> {
         match self {
-            FilePath::System(path) => system_path_to_file(db, path),
-            FilePath::Vendored(path) => vendored_path_to_file(db, path),
+            FilePath::System(path) => system_path_to_file(db, path).ok(),
+            FilePath::Vendored(path) => vendored_path_to_file(db, path).ok(),
             FilePath::SystemVirtual(_) => None,
         }
     }
diff --git a/crates/ruff_db/src/program.rs b/crates/ruff_db/src/program.rs
index 83716ebeae..c5cdc30de6 100644
--- a/crates/ruff_db/src/program.rs
+++ b/crates/ruff_db/src/program.rs
@@ -1,4 +1,5 @@
 use crate::{system::SystemPathBuf, Db};
+use salsa::Durability;
 
 #[salsa::input(singleton)]
 pub struct Program {
@@ -10,7 +11,9 @@ pub struct Program {
 
 impl Program {
     pub fn from_settings(db: &dyn Db, settings: ProgramSettings) -> Self {
-        Program::new(db, settings.target_version, settings.search_paths)
+        Program::builder(settings.target_version, settings.search_paths)
+            .durability(Durability::HIGH)
+            .new(db)
     }
 }
 
diff --git a/crates/ruff_db/src/system/memory_fs.rs b/crates/ruff_db/src/system/memory_fs.rs
index be4406691b..3754a5b9c2 100644
--- a/crates/ruff_db/src/system/memory_fs.rs
+++ b/crates/ruff_db/src/system/memory_fs.rs
@@ -207,7 +207,9 @@ impl MemoryFileSystem {
 
         let normalized = self.normalize_path(path.as_ref());
 
-        get_or_create_file(&mut by_path, &normalized)?.content = content.to_string();
+        let file = get_or_create_file(&mut by_path, &normalized)?;
+        file.content = content.to_string();
+        file.last_modified = FileTime::now();
 
         Ok(())
     }
diff --git a/crates/ruff_db/src/system/test.rs b/crates/ruff_db/src/system/test.rs
index 3a25954224..c5f6dd4060 100644
--- a/crates/ruff_db/src/system/test.rs
+++ b/crates/ruff_db/src/system/test.rs
@@ -1,3 +1,7 @@
+use std::any::Any;
+use std::panic::RefUnwindSafe;
+use std::sync::Arc;
+
 use ruff_notebook::{Notebook, NotebookError};
 use ruff_python_trivia::textwrap;
 
@@ -6,9 +10,6 @@ use crate::system::{
     DirectoryEntry, MemoryFileSystem, Metadata, Result, System, SystemPath, SystemVirtualPath,
 };
 use crate::Db;
-use std::any::Any;
-use std::panic::RefUnwindSafe;
-use std::sync::Arc;
 
 use super::walk_directory::WalkDirectoryBuilder;