(QENG-275) redesign beaker's env var support

- move all env vars reading to options parsing
- rename beaker env vars to match format BEAKER_*name*, still support
  old name format for now
Merge pull request #221 from anodelman/env-fix

(QENG-275) redesign beaker's env var support
(QENG-608) Check_for_package method should not use which command

- properly differentiate between packages and commands
- check_for_package updated to check for the given package name using
  the correct package manager per OS
- added check_for_command, which uses 'which' to determine if a command
  is currently available
- added spec test coverage for check_for_package