Remove extra call to clear_trackers (#13762)

Fixes #13758.

# Objective

Calling `update` on the main app already calls `clear_trackers`. Calling
it again in `SubApps::update` caused RemovedCompenet Events to be
cleared earlier than they should be.

## Solution

- Don't call clear_trackers an extra time.

## Testing

I manually tested the fix with this unit test: 
```
#[cfg(test)]
mod test {
    use crate::core::{FrameCount, FrameCountPlugin};
    use crate::prelude::*;

    #[test]
    fn test_next_frame_removal() {
        #[derive(Component)]
        struct Foo;

        #[derive(Resource)]
        struct RemovedCount(usize);

        let mut app = App::new();
        app.add_plugins(FrameCountPlugin);
        app.add_systems(Startup, |mut commands: Commands| {
            for _ in 0..100 {
                commands.spawn(Foo);
            }
            commands.insert_resource(RemovedCount(0));
        });

        app.add_systems(First, |counter: Res<FrameCount>| {
            println!("Frame {}:", counter.0)
        });

        fn detector_system(
            mut removals: RemovedComponents<Foo>,
            foos: Query<Entity, With<Foo>>,
            mut removed_c: ResMut<RemovedCount>,
        ) {
            for e in removals.read() {
                println!("  Detected removed Foo component for {e:?}");
                removed_c.0 += 1;
            }
            let c = foos.iter().count();
            println!("  Total Foos: {}", c);
            assert_eq!(c + removed_c.0, 100);
        }
        fn deleter_system(foos: Query<Entity, With<Foo>>, mut commands: Commands) {
            foos.iter().next().map(|e| {
                commands.entity(e).remove::<Foo>();
            });
        }
        app.add_systems(Update, (detector_system, deleter_system).chain());

        app.update();
        app.update();
        app.update();
        app.update();
    }
}
```

crates/bevy_app/src/app.rs

@@ -919,14 +919,21 @@ impl Termination for AppExit {
 
 #[cfg(test)]
 mod tests {
-    use std::sync::Mutex;
+    use std::{iter, marker::PhantomData, mem, sync::Mutex};
-    use std::{marker::PhantomData, mem};
 
-    use bevy_ecs::prelude::{Resource, World};
+    use bevy_ecs::{
-    use bevy_ecs::world::FromWorld;
+        change_detection::{DetectChanges, ResMut},
-    use bevy_ecs::{event::EventWriter, schedule::ScheduleLabel, system::Commands};
+        component::Component,
+        entity::Entity,
+        event::EventWriter,
+        query::With,
+        removal_detection::RemovedComponents,
+        schedule::{IntoSystemConfigs, ScheduleLabel},
+        system::{Commands, Query, Resource},
+        world::{FromWorld, World},
+    };
 
-    use crate::{App, AppExit, Plugin, Update};
+    use crate::{App, AppExit, Plugin, SubApp, Update};
 
     struct PluginA;
     impl Plugin for PluginA {
@@ -1129,6 +1136,62 @@ mod tests {
         );
     }
 
+    #[test]
+    fn test_update_clears_trackers_once() {
+        #[derive(Component, Copy, Clone)]
+        struct Foo;
+
+        let mut app = App::new();
+        app.world_mut().spawn_batch(iter::repeat(Foo).take(5));
+
+        fn despawn_one_foo(mut commands: Commands, foos: Query<Entity, With<Foo>>) {
+            if let Some(e) = foos.iter().next() {
+                commands.entity(e).despawn();
+            };
+        }
+        fn check_despawns(mut removed_foos: RemovedComponents<Foo>) {
+            let mut despawn_count = 0;
+            for _ in removed_foos.read() {
+                despawn_count += 1;
+            }
+
+            assert_eq!(despawn_count, 2);
+        }
+
+        app.add_systems(Update, despawn_one_foo);
+        app.update(); // Frame 0
+        app.update(); // Frame 1
+        app.add_systems(Update, check_despawns.after(despawn_one_foo));
+        app.update(); // Should see despawns from frames 1 & 2, but not frame 0
+    }
+
+    #[test]
+    fn test_extract_sees_changes() {
+        use super::AppLabel;
+        use crate::{self as bevy_app};
+
+        #[derive(AppLabel, Clone, Copy, Hash, PartialEq, Eq, Debug)]
+        struct MySubApp;
+
+        #[derive(Resource)]
+        struct Foo(usize);
+
+        let mut app = App::new();
+        app.world_mut().insert_resource(Foo(0));
+        app.add_systems(Update, |mut foo: ResMut<Foo>| {
+            foo.0 += 1;
+        });
+
+        let mut sub_app = SubApp::new();
+        sub_app.set_extract(|main_world, _sub_world| {
+            assert!(main_world.get_resource_ref::<Foo>().unwrap().is_changed());
+        });
+
+        app.insert_sub_app(MySubApp, sub_app);
+
+        app.update();
+    }
+
     #[test]
     fn runner_returns_correct_exit_code() {
         fn raise_exits(mut exits: EventWriter<AppExit>) {

crates/bevy_app/src/sub_app.rs

@@ -125,7 +125,9 @@ impl SubApp {
     }
 
     /// Runs the default schedule.
-    pub fn update(&mut self) {
+    ///
+    /// Does not clear internal trackers used for change detection.
+    pub fn run_default_schedule(&mut self) {
         if self.is_building_plugins() {
             panic!("SubApp::update() was called while a plugin was building.");
         }
@@ -133,6 +135,11 @@ impl SubApp {
         if let Some(label) = self.update_schedule {
             self.world.run_schedule(label);
         }
+    }
+
+    /// Runs the default schedule and updates internal component trackers.
+    pub fn update(&mut self) {
+        self.run_default_schedule();
         self.world.clear_trackers();
     }
 
@@ -421,7 +428,7 @@ impl SubApps {
         {
             #[cfg(feature = "trace")]
             let _bevy_frame_update_span = info_span!("main app").entered();
-            self.main.update();
+            self.main.run_default_schedule();
         }
         for (_label, sub_app) in self.sub_apps.iter_mut() {
             #[cfg(feature = "trace")]

crates/bevy_ecs/src/removal_detection.rs

@@ -116,11 +116,11 @@ impl RemovedComponentEvents {
 ///
 /// If you are using `bevy_ecs` as a standalone crate,
 /// note that the `RemovedComponents` list will not be automatically cleared for you,
-/// and will need to be manually flushed using [`World::clear_trackers`](World::clear_trackers)
+/// and will need to be manually flushed using [`World::clear_trackers`](World::clear_trackers).
 ///
-/// For users of `bevy` and `bevy_app`, this is automatically done in `bevy_app::App::update`.
+/// For users of `bevy` and `bevy_app`, [`World::clear_trackers`](World::clear_trackers) is
-/// For the main world, [`World::clear_trackers`](World::clear_trackers) is run after the main schedule is run and after
+/// automatically called by `bevy_app::App::update` and `bevy_app::SubApp::update`.
-/// `SubApp`'s have run.
+/// For the main world, this is delayed until after all `SubApp`s have run.
 ///
 /// # Examples
 ///

crates/bevy_ecs/src/world/mod.rs

@@ -1113,9 +1113,9 @@ impl World {
     /// By clearing this internal state, the world "forgets" about those changes, allowing a new round
     /// of detection to be recorded.
     ///
-    /// When using `bevy_ecs` as part of the full Bevy engine, this method is added as a system to the
+    /// When using `bevy_ecs` as part of the full Bevy engine, this method is called automatically
-    /// main app, to run during `Last`, so you don't need to call it manually. When using `bevy_ecs`
+    /// by `bevy_app::App::update` and `bevy_app::SubApp::update`, so you don't need to call it manually.
-    /// as a separate standalone crate however, you need to call this manually.
+    /// When using `bevy_ecs` as a separate standalone crate however, you do need to call this manually.
     ///
     /// ```
     /// # use bevy_ecs::prelude::*;