Include note of common profiling issue (#9484)

- Includes a note about a common issue seen when profiling with span
based tracing tools
- Adds a table of contents to profile.md


[Rendered](https://github.com/tbillington/bevy/blob/profiling-doc-update/docs/profiling.md).


[Suggested](https://discord.com/channels/691052431525675048/866787577687310356/1141612079460139108)
by Jasmine on discord.

---------

Co-authored-by: JMS55 <47158642+JMS55@users.noreply.github.com>

docs/profiling.md

@@ -1,22 +1,39 @@
 # Profiling
 
-## Runtime Flame Graph: `tracing` spans
+## Table of Contents
+
+- [Runtime](#runtime)
+ - [Chrome tracing format](#chrome-tracing-format)
+ - [Tracy profiler](#tracy-profiler)
+ - [Adding your own spans](#adding-your-own-spans)
+ - [Perf flame graph](#perf-flame-graph)
+- [Compile time](#compile-time)
+
+## Runtime
 
 Bevy has built-in [tracing](https://github.com/tokio-rs/tracing) spans to make it cheap and easy to profile Bevy ECS systems, render logic, engine internals, and user app code. Enable the `trace` cargo feature to enable Bevy's built-in spans.
 
 If you also want to include `wgpu` tracing spans when profiling, they are emitted at the `tracing` `info` level so you will need to make sure they are not filtered out by the `LogSettings` resource's `filter` member which defaults to `wgpu=error`. You can do this by setting the `RUST_LOG=info` environment variable when running your application.
 
-You also need to select a `tracing` backend using the following cargo features:
+You also need to select a `tracing` backend using one of the following cargo features.
+
+**⚠️ Note**: for users of [span](https://docs.rs/tracing/0.1.37/tracing/index.html) based profilers
+
+When your app is bottlenecked by the GPU, you may encounter frames that have multiple prepare-set systems all taking an unusually long time to complete, and all finishing at about the same time.
+
+Improvements are planned to resolve this issue, you can find more details in the doc comment for [`prepare_windows`](../crates/bevy_render/src/view/window/mod.rs).
+
+![prepare_windows span bug](https://github.com/bevyengine/bevy/assets/2771466/15c0819b-0e07-4665-aa1e-579caa24fece)
 
-### Backend: trace_chrome
+### Chrome tracing format
 
 `cargo run --release --features bevy/trace_chrome`
 
 After running your app a `json` file in the "chrome tracing format" will be produced. You can open this file in your browser using <https://ui.perfetto.dev>. It will look something like this:
 
 ![image](https://user-images.githubusercontent.com/2694663/141657409-6f4a3ad3-59b6-4378-95ba-66c0dafecd8e.png)
 
-### Backend: trace_tracy
+### Tracy profiler
 
 The [Tracy profiling tool](https://github.com/wolfpld/tracy) is:
 > A real time, nanosecond resolution, remote telemetry, hybrid frame and sampling profiler for games and other applications.
@@ -78,19 +95,19 @@ Search for `info_span!` in this repo for some real-world examples.
 
 For more details, check out the [tracing span docs](https://docs.rs/tracing/*/tracing/span/index.html).
 
-## `perf` Runtime Flame Graph
+### `perf` Flame Graph
 
 This approach requires no extra instrumentation and shows finer-grained flame graphs of actual code call trees. This is useful when you want to identify the specific function of a "hot spot". The downside is that it has higher overhead, so your app will run slower than it normally does.
 
 Install [cargo-flamegraph](https://github.com/flamegraph-rs/flamegraph), [enable debug symbols in your release build](https://github.com/flamegraph-rs/flamegraph#improving-output-when-running-with---release), then run your app using one of the following commands. Note that `cargo-flamegraph` forwards arguments to cargo. You should treat the `cargo-flamegraph` command as a replacement for `cargo run --release`. The commands below include `--example EXAMPLE_NAME` to illustrate, but you can remove those arguments in favor of whatever you use to run your app:
 
-* Graph-Like Flame Graph: `RUSTFLAGS='-C force-frame-pointers=y' cargo flamegraph -c "record -g" --example EXAMPLE_NAME`
-* Flat-ish Flame Graph: `RUSTFLAGS='-C force-frame-pointers=y' cargo flamegraph --example EXAMPLE_NAME`
+- Graph-Like Flame Graph: `RUSTFLAGS='-C force-frame-pointers=y' cargo flamegraph -c "record -g" --example EXAMPLE_NAME`
+- Flat-ish Flame Graph: `RUSTFLAGS='-C force-frame-pointers=y' cargo flamegraph --example EXAMPLE_NAME`
 
 After closing your app, an interactive `svg` file will be produced:
 ![image](https://user-images.githubusercontent.com/2694663/141657609-0089675d-fb6a-4dc4-9a59-871e95e31c8a.png)
 
-## Project Compile Times
+## Compile time
 
 Append `--timings` to your app's cargo command (ex: `cargo build --timings`).
 If you want a "full" profile, make sure you run `cargo clean` first (note: this will clear previously generated reports).