vagrant/run_bootstrap.sh: Removed nptdate call that was not working.
vagrant/bootstrap.sh: Added code to automatically initialize Makahiki during provisioning.
vagrant/doc/ubuntu_x86_vagrant_readme.txt: General cleanup; removed Notepad++ related instructions; moved Makahiki initialization into an appendix.
vagrant/doc/ubuntu_x86_vagrant_readme.txt: Added warning about dpkg-preconfigure.
Merge pull request #554 from jtakayama/master

The bootstrap.sh script now initializes the database.