solve #306, and bin in $PATH make sense now

solve #306, and bin in $PATH make sense now  #196
Almost revert #173 which lead to the bug in #306

Also remove deprecated `customFds` option in spawn
It's [deprecated](https://github.com/iojs/io.js/commit/56785958565378c9ba43c5bdf5c631f7738f95ab).