diff --git a/src/files.rs b/src/files.rs
index 8e837759..d4bb63b8 100644
--- a/src/files.rs
+++ b/src/files.rs
@@ -104,15 +104,15 @@ fn collect_changed_names(
     let mut names: std::collections::BTreeSet<String> = Default::default();
 
     // Committed changes in the range.
-    for line in git_diff_names(project_root, &["--diff-filter=d", &range])? {
+    for line in git_diff_names(project_root, &[&range])? {
         names.insert(line);
     }
     // Unstaged changes.
-    for line in git_diff_names(project_root, &["--diff-filter=d"])? {
+    for line in git_diff_names(project_root, &[])? {
         names.insert(line);
     }
     // Staged changes.
-    for line in git_diff_names(project_root, &["--cached", "--diff-filter=d"])? {
+    for line in git_diff_names(project_root, &["--cached"])? {
         names.insert(line);
     }
 
diff --git a/src/linters/renovate_deps.rs b/src/linters/renovate_deps.rs
index ca95e58f..acf29621 100644
--- a/src/linters/renovate_deps.rs
+++ b/src/linters/renovate_deps.rs
@@ -127,15 +127,7 @@ pub(crate) fn is_relevant(file_list: &FileList, project_root: &Path) -> bool {
         return true;
     }
 
-    let changed: HashSet<String> = file_list
-        .files
-        .iter()
-        .filter_map(|path| {
-            path.strip_prefix(project_root)
-                .ok()
-                .map(|rel| rel.to_string_lossy().into_owned())
-        })
-        .collect();
+    let changed = changed_rel_paths(file_list, project_root);
 
     if changed.is_empty() {
         return false;
@@ -173,6 +165,34 @@ pub(crate) fn is_relevant(file_list: &FileList, project_root: &Path) -> bool {
     committed.keys().any(|path| changed.contains(path))
 }
 
+fn changed_rel_paths(file_list: &FileList, project_root: &Path) -> HashSet<String> {
+    if !file_list.changed_paths.is_empty() {
+        return file_list
+            .changed_paths
+            .iter()
+            .map(|path| {
+                let path = Path::new(path);
+                path.strip_prefix(project_root).unwrap_or(path)
+            })
+            .map(normalize_path)
+            .collect();
+    }
+
+    file_list
+        .files
+        .iter()
+        .filter_map(|path| path.strip_prefix(project_root).ok())
+        .map(normalize_path)
+        .collect()
+}
+
+fn normalize_path(path: &Path) -> String {
+    path.components()
+        .map(|component| component.as_os_str().to_string_lossy())
+        .collect::<Vec<_>>()
+        .join("/")
+}
+
 pub(crate) fn adaptive_relevance(ctx: &dyn AdaptiveRelevanceContext) -> bool {
     is_relevant(ctx.file_list(), ctx.project_root())
 }
@@ -514,10 +534,7 @@ fn committed_path_for_config(config_path: &Path) -> PathBuf {
 }
 
 fn display_path(project_root: &Path, path: &Path) -> String {
-    path.strip_prefix(project_root)
-        .unwrap_or(path)
-        .to_string_lossy()
-        .into_owned()
+    normalize_path(path.strip_prefix(project_root).unwrap_or(path))
 }
 
 /// Parses Renovate's NDJSON log and returns the dep map.
@@ -967,6 +984,19 @@ mod tests {
         assert!(diff.contains("renovate-tracked-deps.json"));
     }
 
+    #[test]
+    fn display_path_normalizes_separators() {
+        let dir = tempfile::tempdir().unwrap();
+        let path = dir
+            .path()
+            .join(".github")
+            .join("renovate-tracked-deps.json");
+        assert_eq!(
+            display_path(dir.path(), &path),
+            ".github/renovate-tracked-deps.json"
+        );
+    }
+
     #[test]
     fn resolves_supported_renovate_config_file() {
         let dir = tempfile::tempdir().unwrap();
@@ -1071,6 +1101,26 @@ mod tests {
         ));
     }
 
+    #[test]
+    fn relevant_when_tracked_manifest_was_deleted() {
+        let dir = tempfile::tempdir().unwrap();
+        std::fs::create_dir_all(dir.path().join(".github")).unwrap();
+        write_snapshot(
+            &dir.path().join(".github/renovate-tracked-deps.json"),
+            &dep_map(&[("package.json", &[("npm", &["express"])])]),
+        )
+        .unwrap();
+
+        let file_list = FileList {
+            files: vec![],
+            changed_paths: vec!["package.json".to_string()],
+            merge_base: Some("base".to_string()),
+            full: false,
+        };
+
+        assert!(is_relevant(&file_list, dir.path()));
+    }
+
     #[test]
     fn not_relevant_for_untracked_change() {
         let dir = tempfile::tempdir().unwrap();
diff --git a/tests/e2e.rs b/tests/e2e.rs
index e7cf233a..1c36d531 100644
--- a/tests/e2e.rs
+++ b/tests/e2e.rs
@@ -164,6 +164,115 @@ fn cases() {
     }
 }
 
+// Unix-only: this e2e test creates a fake linter as a POSIX shell script and
+// marks it executable with Unix permissions.
+#[cfg(unix)]
+#[test]
+fn renovate_deps_fast_only_runs_for_deleted_tracked_file() {
+    let repo = git_repo();
+
+    std::fs::create_dir_all(repo.path().join(".github")).unwrap();
+    std::fs::write(
+        repo.path().join("mise.toml"),
+        r#"[tools]
+node = "22.0.0"
+
+# Linters
+"npm:renovate" = "43.136.3"
+"#,
+    )
+    .unwrap();
+    std::fs::write(repo.path().join(".github/renovate.json5"), "{}\n").unwrap();
+    std::fs::write(repo.path().join("package.json"), "{}\n").unwrap();
+    std::fs::write(
+        repo.path().join(".github/renovate-tracked-deps.json"),
+        r#"{
+  "package.json": {
+    "npm": [
+      "express"
+    ]
+  }
+}
+"#,
+    )
+    .unwrap();
+
+    let out = Command::new("git")
+        .args(["add", "-A"])
+        .current_dir(repo.path())
+        .output()
+        .expect("failed to spawn git add");
+    assert!(
+        out.status.success(),
+        "git add failed: {}",
+        String::from_utf8_lossy(&out.stderr)
+    );
+    let out = Command::new("git")
+        .args(["commit", "-q", "-m", "init"])
+        .current_dir(repo.path())
+        .output()
+        .expect("failed to spawn git commit");
+    assert!(
+        out.status.success(),
+        "git commit failed: {}",
+        String::from_utf8_lossy(&out.stderr)
+    );
+
+    let out = Command::new("git")
+        .args(["rm", "-q", "package.json"])
+        .current_dir(repo.path())
+        .output()
+        .expect("failed to spawn git rm");
+    assert!(
+        out.status.success(),
+        "git rm failed: {}",
+        String::from_utf8_lossy(&out.stderr)
+    );
+
+    let fake_bin_dir = tempfile::tempdir().expect("fake_bin tempdir");
+    let renovate = fake_bin_dir.path().join("renovate");
+    std::fs::write(
+        &renovate,
+        r#"#!/bin/sh
+set -eu
+
+touch .renovate-ran
+printf '%s\n' '{"msg":"Extracted dependencies","packageFiles":{"mise":[{"packageFile":"mise.toml","deps":[{"depName":"npm:renovate"}]}]}}'
+"#,
+    )
+    .unwrap();
+
+    use std::os::unix::fs::PermissionsExt;
+    std::fs::set_permissions(&renovate, std::fs::Permissions::from_mode(0o755)).unwrap();
+
+    let fake_path = format!(
+        "{}:{}",
+        fake_bin_dir.path().display(),
+        std::env::var("PATH").unwrap_or_default()
+    );
+    let out = flint_with_env(
+        &["run", "--fast-only"],
+        repo.path(),
+        &[("PATH", &fake_path)],
+    );
+
+    assert!(
+        repo.path().join(".renovate-ran").exists(),
+        "renovate-deps was skipped; stdout:\n{}\nstderr:\n{}",
+        String::from_utf8_lossy(&out.stdout),
+        String::from_utf8_lossy(&out.stderr)
+    );
+    assert_eq!(
+        out.status.code(),
+        Some(1),
+        "expected stale renovate snapshot failure; stdout:\n{}\nstderr:\n{}",
+        String::from_utf8_lossy(&out.stdout),
+        String::from_utf8_lossy(&out.stderr)
+    );
+}
+
+// Unix-only: this e2e test creates fake linters as POSIX shell scripts and
+// marks them executable with Unix permissions.
 #[cfg(unix)]
 #[test]
 fn markdown_tool_ignores_biome_owned_jsonc() {
@@ -336,6 +445,8 @@ exit 1
     );
 }
 
+// Unix-only: this e2e test creates a fake linter as a POSIX shell script and
+// marks it executable with Unix permissions.
 #[cfg(unix)]
 #[test]
 fn rumdl_fix_hides_success_noise_when_another_file_fails() {