he/him 
If you have a dependency that exposes binaries with @npmjs then removing that dep is a semver major since it's breaking as npm puts... [1/2]
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Removing a bin could result in something else slotting in there, but removing a bin IS a breaking change regardless.
sure, for the transitive dep but my point is that transitive dep binaries are now a part of your own libraries API contract
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Calling some transitive dep's binaries is like requiring some transitive dep. You _can_ do it, but you get to keep the pieces.
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I don't go trawling through node_modules/.bin for things to run. I get them from docs of things I required. I dunno about you. =D
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It probably would be worth having a linter for this kind of though though.
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All this said, I'm not opposed to the idea of giving each module its own set of node_modules/.bin links, for clarity.
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