Preserve Custom Lambda Layers

First of all: Chalice is amazing! Great Job!

Now the "issue":

I have a third party Lambda Layer that I add to all my Lambda functions.
I have a Chalice project with `automatic_layer: True` so it is creating a Lambda Layer with shared code.
After each `chalice deploy` I have to add my third party Lambda Layer again to all my Lambda functions.
Could `chalice deploy` check for custom Lambda Layers that are not generated by Chalice and re-apply them after a new version was deployed?

This would be great!

Start by locating Chalice's deployment handling for projects with `automatic_layer: True` and trace how Lambda function layers are updated during `chalice deploy`. Determine how manually attached third-party layers can be identified and preserved, then verify that a redeploy retains them on every function.

Written by the indexing model from the issue text.