Use MySQLdb instead of pymysql

* App Engine uses MySQLdb; pymysql has disconnection issues,
  so remote pymysql dependency and rewrite default database
  connection strings
* add bin/setup_linked_packages.py to inspect location of
  installed packages and link into development PYTHONPATH
* add setup_linked_packages to Makefile's "setup_dev" task
* invoke "make setup_dev" from Chef recipe
* remove "git submodule update --init" from "setup_dev" task,
  since it needs to be done from non-VM side