Issue with beanstalk and cloudformation

Parden me if I'm asking dumb questions.

So for beanstalk, my current folder structure is like this:
which the extension does is add https binding and add environment variable("Development, Staging etc"), now I manage to build out this structure through TeamCity. Somehow the breanstalk step package up the bundle and generates aws-windows-deployment-manifest.json by itself and not include my extension script which failed my deployment
, how can I fix this?

2nd question about cloudformation. My cloudformation template are nested, and I refer them in my main template:
without uploading them to s3, how the create/update stack task knows where to find my sub-templates?
What should I put on my bases3repo variable instead of my s3 bucket url(since it will be running on vsts build agent now)?

Thank you for your time.

Start by reproducing the TeamCity/VSTS build-agent packaging flow and inspect the generated aws-windows-deployment-manifest.json and missing extension script. Then trace how the nested CloudFormation templates are referenced during create/update and determine what value bases3repo should use. Done means both deployment packaging and nested-template resolution work without the reported failure.

Written by the indexing model from the issue text.