Bevy's default App::update() is limiting for subapp workflows.

## What problem does this solve or what need does it fill?
Currently you're restricted to Bevy's default update and extract workflow, which is limiting for more complex workflows using subapps.

## What solution would you like?
Currently, the simple solution seems like the best solution, which is to allow the user to replace App::update() with their own function. This would allow the user to then iterate subapps themselves and manually call extract as needed.

## What alternative(s) have you considered?

I honestly couldn't think of anything that couldn't just be implemented in terms of replacing App::update()

An explicit extract flow graph for example (to allow the user to specify which apps extract from where) could just be done with the above solution instead.

Willing to pick this up and implement it myself to meet the 0.16.x release cycle.

Start by tracing Bevy's App::update() entry point and the existing subapp and extract workflow. Define done as allowing callers to replace the default update flow, iterate subapps themselves, and invoke extraction as needed, while preserving the stated alternative workflows.

Written by the indexing model from the issue text.