I don't think it is possible, https://www.npmjs.org/doc/files/npm-folders.html states that the modules should be in node_modules .
For your purposes, you can copy everything except the node_modules folder and make npm install --production in the new copied folder, so that there will be only production dependencies in the assembly.
This should do what you want, without much work:
rsync -av --progress yourproject yourbuilddir --exclude node_modules cd yourbuilddir && npm install --production
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