deps: remove and gitignore .bin directory

The .bin/ directory in deps/npm/node_modules seens to have been an
accidental check-in in commit e79ccee1 ("npm: upgrade to v2.1.18").
It causes trouble for distro packagers so delete it and blacklist it.

Fixes: https://github.com/nodejs/node/issues/2839
PR-URL: https://github.com/nodejs/node/pull/3004


Reviewed-By: Kat Marchán <kzm@sykosomatic.org>
Reviewed-By: Rod Vagg <r@va.gg>
Reviewed-By: Sakthipriyan Vairamani <thechargingvolcano@gmail.com>