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
R=@rvagg? /cc @othiym23