Use %P for all sensitive command construction in Phabricator

Summary: Depends on D6366. Applies %P everywhere.

Test Plan: Ran various daemon commands via scripts, e.g. `bin/repository pull`, `bin/storage dump`.

Reviewers: btrahan, mbishopim3

Reviewed By: btrahan

CC: aran

Differential Revision: https://secure.phabricator.com/D6367