Dependency trace does not capture code system dependencies of direct-reference codes

[brynrhodes]

The dependency trace logic used in at least $release and $package, potentially $data-requirements as well, is not reporting the code system of a direct-reference code as a dependency.

This resulted in code systems referenced only from direct-reference codes not being included in the ecqm-fhir-update-2025 manifest.

https://github.com/cqframework/dqm-content-qicore-2025/blob/master/input/resources/library/Library-ecqm-fhir-update-2025.json

Note that the issue is being corrected manually for the public comment review release, so this doesn't need to be addressed urgently, but it is an issue that needs to be fixed.