Revert "Revert "adding exclude files + other changes to get registration to work for me""

[Tofel]

This pull request restores important proto dependency features and updates a test reference in the framework package. The main focus is on bringing back topological sorting and support for exclude files in proto registration, which are essential for correct proto dependency management.

Proto dependency management improvements:

• Restored topological sorting of proto dependencies for the local-cre process to ensure correct build order.
• Reintroduced support for exclude files in proto registration configuration, allowing selective exclusion of files from proto registration.

Test updates:

• Updated the Ref for the proto schema set in smoke_chip_ingress_test.go to point to a newer commit, ensuring tests use the latest proto definitions.

Successful test run: https://github.com/smartcontractkit/chainlink-testing-framework/actions/runs/17373213916/job/49313659087?pr=2081