Repro of stuff in node_modules/.bin disappearing with npm-ci

package.json

{
    "name": "npm-ci-repro",
    "version": "1.0.0",
    "description": "",
    "main": "index.js",
    "scripts": {
        "test": "rm -rf node_modules package-lock.json && npm i && ls node_modules/.bin && npm ci && ls node_modules/.bin"
    },
    "keywords": [],
    "license": "ISC",
    "devDependencies": {
        "json2csv": "3.11.5",
        "npm-run-all": "4.1.2"
    },
    "dependencies": {
        "d3": "4.11.0"
    }
}

Seems it will only reproduce if the colliding binary-names comes from a transitive dependency. In this case it is d3-dsv which provides the binaries that collides with json2csv.

Adding the transitive dependency as a proper dependency seems to solve the issue

Also, the state of the local npm-cache seems to effect the outcome. If I add the transitive dep as a proper dep, install, and then remove the transitive dep again the bug will not reproduce.

Also, this is on macOS 10.13.3, with node v 8.9.4 and npm 5.7.0