What version of dep are you using (dep version)?

v0.4.0

What dep command did you run?

dep ensure

Gopkg.toml contains per-project prune options which are silently ignored.
Global options have non-go pruning enabled, per-project options has non-go pruning disabled.

What did you expect to see?

Per-project prune options applied, non-go files not pruned for specific project.

What did you see instead?

Global prune options are applied to every project.

Analysis

A quick analysis of this issue shows that fromRawPruneOptions incorrectly applies the global options (from raw, instead of from p) when converting the raw prune options to gps.RootPruneOptions.

I am in the process of preparing a PR with a fix for this problem right now.