add ability to set publish ports to `config.yml`

[leehinman]

Previously we could edit snapshot.yml and change the publish ports to do things like listen on a different network interface from localhost. With #1140 we can't do that anymore because snapshot.yml gets overwritten every time "stack up" is called.

Use Case: When testing different OSes, for example you want the stack running on Linux, but an elastic-agent running on Windows.