When you want to have a clean package, you must put dev tool list and version in devDependencies in your package.json, for example :
"devDependencies": {
"gulp": "^3.8.8",
"bower": "^1.8.0"
}
However, node-which which is used to check if the binary is present doesn't check in this folder since ./node_modules/.bin/ is unlikely to be in your path.
A workaround is to run with a prefixed export like this :
PATH=$PATH:./node_modules/.bin/ ./node_modules/.bin/gulp
But I think it would be a better solution to check in .node_modules/.bin/