Fix method visibility for PhabricatorApplication methods

Summary: Ref T6822.

Test Plan: Visual inspection. These methods are only called from within the PhabricatorApplication class.

Reviewers: #blessed_reviewers, epriestley

Reviewed By: #blessed_reviewers, epriestley

Subscribers: Korvin, epriestley

Maniphest Tasks: T6822

Differential Revision: https://secure.phabricator.com/D11243