Meteor ignore node_modules

I'm building an IRC bot (backed by MongoDB) and I want to give it a web interface on my server (not meteor.com). I want to use meteor because of the live-updating and because I want to learn how to use it.

For meteor to recognize that I have other subfolders that might have web interfaces (some modules will have web interfaces, and some will not), I need to have meteor run from the application root. When I do that, meteor looks inside my node_modules folder and determines that it can't run the same file twice (some duplicate dependency), then it crashes.

I either need to ignore node_modules when I run meteor, or move node_modules to a subdirectory (like meteor's lib/). I'm pretty sure I can't make npm install do that though, so what can I do?

I keep seeing people wishing for a .meteorignore, and I'm feeling that too.

For now I think the best solution is to introduce another folder between the root and the modules and setup meteor there, but I'll leave this open in case others have better ideas.