• Runtime pack dependencies in deps.json and in the DependencyContext model have a "runtimepack." prefix prependend to the nuget package id (see 16eddf3#diff-0723634e548f98293eebe3970b71e0ddR328).
• The heuristic in GetPackageParts gets the package id from the name of a nuspec in a parent directory:
  

  sdk/src/Tasks/Common/NuGetUtils.cs

  Lines 48 to 52 in ab2176b

  	var nuspecs = dir.GetFiles("*.nuspec");
  	if (nuspecs.Length > 0)
  	{
  	packageId = Path.GetFileNameWithoutExtension(nuspecs[0].Name);

GenerateDepsFile uses GetPackageParts to build the list of packages with dependencies to remove. When it looks for files to trim from the dependency model, it doesn't match any of the dependencies that have the "runtimepack." prefix, so those files don't get skipped.