Can't we just make `bin/server.js` executable?

I don't mind setting the executable bit, but I mind the mixing of executables and non-executables in `bin/` folder. ie. right now `server.js` is not an executable.

I think we should make `server.js` executable, and add utilities as other executables as we need them. Specifically, I don't feel good wrapping the server in commander.js. I have some mixed feelings about commander.js, it's probably fine for writing utilities with related methods.
But let's not stuff everything into one binary, in particular the server should not be mixed with utilities.