So in my Install.ps1 I can add a reference like this:
param($installPath, $toolsPath, $package, $project) $project.Object.References.Add(\"YourDLL\")
Here's what we use for Machine.Specifications:
param($installPath, $toolsPath, $package, $project) $project.Object.References | Where-Object { $_.Name -eq 'Machine.Specifications.TDNetRunner' } | ForEach-Object { $_.Remove() }