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This isn't a bug nor an issue, however I'm curious why you chose to make node-pre-gyp a bundled dependency.
I noticed because despite only one occurrence of node-pre-gyp in my dependency tree, npm (v3+) didn't flatten it into the root of my node_modules. I'm assuming that's because it's a bundled dependency.
I found this same non-flattening behavior with jstransform and esprima-fb but in that case esprima-fb is not a bundled dependency of jstransform, so there must be a different cause in that case.