tools: Fix copying contents of deps/npm

This fixes a platform inconsistency between BSD and GNU `cp` where
`deps/npm` would be copied into a subdirectory of `test-npm` on Linux,
but not on OS X.

PR-URL: https://github.com/nodejs/io.js/pull/1853


Reviewed-By: Roman Reiss <me@silverwind.io>
Reviewed-By: Johan Bergström <bugs@bergstroem.nu>