Update bad links in `/pkg` examples

[a-poor]

The examples in the project-layout/pkg/README.md file include repositories with links that should be updated (renamed branches) and repositories that should be removed (no longer include a /pkg directory):

Repositories that no longer include a /pkg directory:

• prometheus/prometheus
• minio/minio

Repositories with renamed main branches:

• jaegertracing/jaeger (renamed master branch to main)
• GoogleContainerTools/kaniko (renamed master branch to main)
• helm/helm (renamed master branch to main)
• grafana/grafana (renamed master branch to main)
• etcd-io/etcd (renamed master branch to main)
• GoogleContainerTools/skaffold (renamed master branch to main)
• knative/serving (renamed master branch to main)
• grafana/loki (renamed master branch to main)
• DataDog/datadog-agent (renamed master branch to main)
• dapr/dapr (renamed master branch to main)
• weaveworks/kured (renamed master branch to main)
• weaveworks/footloose (renamed master branch to main)
• weaveworks/ignite (renamed master branch to main)