Removed assemblies should be remembered

Upgrade Planner allows removing assemblies. We currently completely remove them and forget that we ever had them. Very often these are 3rd party components which we don't want to analyze and know they are support (for example, xUnit or other well-known NuGet packages).

This causes noise as we also report missing dependencies and the removed assemblies are now showing up as unresolved.

Instead, we should remember the removed assemblies and excluded them from missing dependencies. This still catches inadvertent exclusions while not causing noise for intentional removals.

Start by tracing how the Upgrade Planner removes assemblies and how it reports missing dependencies. Make removed assemblies persist as exclusions and ensure they are omitted from missing-dependency results while other inadvertent exclusions remain detectable; verify the behavior with the project's existing tests.

Written by the indexing model from the issue text.