[CB-4065] Remove lib files after frameworkModules.js is generated

  Reviewed By: Jeffrey Heifetz <jheifetz@blackberry.com>
  Tested By: Tracy Li <tli@blackberry.com>
[CB-4544] Adds a --query flag to query the user for their password when we need it
 - Rewrite the run script for maintenance

  Reviewed By: Bryan Higgins <bhiggins@blackberry.com>
  Tested By: Tracy Li <tli@blackberry.com>