When I create a Package with the Package Manager I can check the Node Library files explicitly. In previous versions of Dynamo the pkg.json only referred to those files, not other added library files. But in Dynamo 2.13 all library files are included as node libraries in the pkg.json, even the files I did not checkmarked.
The package seems to work though but I am not sure if that is by accident or that the checkmarks doesn’t matter (anymore).
After some tests there are issues. The extra libraries are not visible in the category list but the functions can be called from DesignScript. So they are loaded as library files.
Hello @Anton_Huizinga - this seems like a bug from your description. Are you able to please post the steps you are taking, and attach the pkg.json file here so we can take a look and try and reproduce?
These are the steps:
I checkmarked two files that are node libraries, the others are references and should not be loaded by Dynamo.
It is saved successfully but if you open the pkg.json you can see all libraries are marked as node libraries:
If I take all these steps in Civil 3D 2022 or 2020, only the selected libraries are marked as node libraries, like expected.
Thank you for the reproduction steps @Anton_Huizinga - We’re looking into it now, but it very much appears like a bug that we’ll need to fix. If so, that will target our next release (2.15).
Our sincerest apologies for missing this bug and causing this issue 
@Anton_Huizinga - We’ve looked into this today, and can’t seem to reproduce on our end. We are testing here using Dynamo Revit. Does the GIF take any steps that are different to your own?
If not, then we may be looking at a specific Civil 3d implementation bug. We’ll continue to look deeper
It must be Civil 3D specific I guess:
Btw: If I do exactly the same in older Dynamo versions, it works as expected.
@Anton_Huizinga one of our developers has managed to reproduce the same case you have - definitely a bug, just not ubiquitous. We’re looking into it further
Thanks 
We have a fix submitted for the Dynamo 2.15 release on this @Anton_Huizinga - please refer to Mark Node Library Correctly by QilongTang · Pull Request #12887 · DynamoDS/Dynamo · GitHub 
Thanks!
