Minor doc update
Include tools to download pkg sources for all installed packages
Add MOTD updates
Convert apache site to use SSL.

Includes self-signed SSL certs which should be considered insecure,
but easily replaceable with real certs and instructions on how to
generate new ones.
Add scheduler template files and supervisord config
Add upgrade and convert functions to vm_env
Cleanup missing directories
Add README and LICENSE, update motd on login
Install steelscript directly, fix ipython notebook

Also update installed package list, and clarify
security updates needed.
Update default scheduler cfg; add toggle_scheduler
Update USAGE docs
Update source download scripts and READMEs
Add helper script
Fix readme link