Update `Bender.yml`

Created by: niwis

This is required (in some form) by #1024.

Most PULP systems (like Ara) use bender for dependency and source file management.

Problem: the current Bender.yml directly includes the vendored IPs (e.g. common cells). However, if common cells is also listed as a dependency of the system, this causes redefinitions of the same module.

Solution: do not include the vendored dependencies in Bender.yml, but add them as a bender dependency. We track the vendored revision in Bender.lock to stay in sync.

I know it's not a perfect solution, but it should be non-breaking since afaik Bender.yml is not used anywhere within this repo.

Adding @joennlae who authored the changes and validated them in Cheshire.