Reputation is the per-character (or per-squad) modifier that sits on top of the faction baseline. A Bovarian docker might belong to faction Civilian (Neutral to your squad) but personally regard your medic as a friend, dragging the effective stance toward Friendly for any opposed checks involving them.
Page status; stub. Reputation is rolled out alongside the Faction system (GH #11). Until then, GMs handle individual standing narratively.