refactor: update AppState references to use state module

- Change all instances of AppState to reference the new state module across multiple files for consistency.
- Clean up imports in auth, books, index_jobs, libraries, pages, search, settings, thumbnails, and tokens modules.
- Simplify main.rs by removing unused code and organizing middleware and route handlers under the new handlers module.

apps/api/src/api_middleware.rs

@@ -0,0 +1,42 @@
+use axum::{
+    extract::State,
+    middleware::Next,
+    response::{IntoResponse, Response},
+};
+use std::time::Duration;
+use std::sync::atomic::Ordering;
+
+use crate::state::AppState;
+
+pub async fn request_counter(
+    State(state): State<AppState>,
+    req: axum::extract::Request,
+    next: Next,
+) -> Response {
+    state.metrics.requests_total.fetch_add(1, Ordering::Relaxed);
+    next.run(req).await
+}
+
+pub async fn read_rate_limit(
+    State(state): State<AppState>,
+    req: axum::extract::Request,
+    next: Next,
+) -> Response {
+    let mut limiter = state.read_rate_limit.lock().await;
+    if limiter.window_started_at.elapsed() >= Duration::from_secs(1) {
+        limiter.window_started_at = std::time::Instant::now();
+        limiter.requests_in_window = 0;
+    }
+
+    if limiter.requests_in_window >= 120 {
+        return (
+            axum::http::StatusCode::TOO_MANY_REQUESTS,
+            "rate limit exceeded",
+        )
+            .into_response();
+    }
+
+    limiter.requests_in_window += 1;
+    drop(limiter);
+    next.run(req).await
+}