Merge branch 'master' into develop

* master:
  change how secret_token is set by vagrant
  change template for settings.yml for mail configuration
  ALM-572 made alm Chef script non-destructive so that it can be used to update alm installations
  updated to newest versions of external cookbooks
  ALM-564 updated documentation
  ALM-399 hide slow functions from admin dashboard for more than 150,000 articles
  Set default Reddit rate-limiting to 1800/hr. Closes #25
  Fixed typo in documentation
  require d3.js library
  change javascript load order
  precompile all javascript files in production
ALM-575 removed legacy code from v2 API
Don't start calling CrossRef until one day after publication. Closes #26
Make :warn the standard log level in production. Closes #27
Merge branch 'refs/heads/develop'