fix: resolve CI failures (fmt, clippy, tests)

- Fix rustfmt formatting in cache.rs, patches.rs, system.rs, routes.rs, main.rs
- Add Default impl for PackageCacheState (clippy new_without_default)
- Change apply_with_cache_retry generic bound from Fn to FnMut
- Add mut to refresh_fn parameter for FnMut compatibility
- Replace bool comparison with ! operator (clippy bool_comparison)
- Update todo.md with completed status

src/main.rs

@@ -166,7 +166,12 @@ async fn main() -> Result<()> {
 
         // Configure API routes
         app = app.configure(|cfg| {
-            configure_api_routes(cfg, job_manager_data.clone(), backend_data.clone(), cache_state.clone());
+            configure_api_routes(
+                cfg,
+                job_manager_data.clone(),
+                backend_data.clone(),
+                cache_state.clone(),
+            );
         });
 
         // Configure health route (outside API scope)