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Fix method visibility for `PhabricatorApplication` methods

Description

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