Update bin/rails bin/bundle and bin/rake

Using

bundle exec rake rails:update:bin

previously they did not have the executable bit, and contained
'ruby.exe', which cannot work on non-windows machines, wheres with now
just 'ruby' it might also work on windows, in any case it looks more
correct that way.

Bottom line: you can use

bin/rails s

instead of

bundle exec rails s

now to save you some typing. Unless of course simply

rails s

works for you, then that's fine too.