#232: server: moved files;
#232: bin: moved files
#232: service: remove app.js
#232: add deps on `open`; adjust path according to the changes of dirs
#232: service/logger: use the same logger as CLI directly
#232: service/neuropil: use the same neuropil config as cli directly
#232: service/static: fix codes with open
#232: refractored cortex server and its middlewares