Fix branch ordering on dynamic reconfiguration

Change I425395db19cc6b336a2db9cf46415d8a5f4c036f corrected the
branch ordering when loading in-repo configuration, however, it
lacked a fix for the case when dynamic reconfiguration only loaded
part of the config anew.

This ensures that we load configuration from branches in the correct
order even under dynamic reconfiguration.

Change-Id: Id1266a5d553f88d9354b259d523821a707d4ac98
2 files changed