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I was able to do this in an earlier version of nDepend by going to tools->options and setting which assemblies would be part of the analysis (and ignore the rest). The latest version of the trial version of nDepend lets me set it, but it seems to ignore the setting and always analyze all assemblies whether I want it to or not. I tried to delete the "tier" assemblies by moving them over to the "application assemblies" list, but when I delete them out of there, they just get added back to the "tier" list, which I can't ignore.

I don't want my dependency graph to contain assemblies like "system," "system.xml," and "system.serialization!" I want only MY assemblies in the dependency graph! Or is that a paid-version feature now?

Is there a way to do what I'm talking about?

A: 

Tier assemblies are indeed now automatically inferred and added to the NDepend project. This relieves NDepend users from the burden of doing that manually. The side-effect you describe is that tier assemblies appear in the dependency graph generated in the report.

Your 2 options to get a graph without tier assemblies are:

-> In the NDepend project file, delete tier assemblies manually (those in the XML tag). This trick will automatically remove tier assemblies from the report graph.

-> Generate manually the graph with the set of assemblies you wish, from the VisualNDepend UI.

Patrick Smacchia - NDepend dev