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The Combine offers a way to keep track of all your relations, be they hostile or friendly. The tool to do this is called the IFF list, or Identify Friend/Foe list. The link can be found on your character screen.
Adding people to your IFF list is done by typing their name in the respective box and pressing 'Add'. The character is now considered your ally/enemy for all purposes such as scanning (see scanning rules for more).
Factions can also be added to the lists. In a case where a faction and character have conflicting entries, the character's entry will override the faction entry.
To determine who is your Friend (or Foe), the following checks are processed:
If all checks failed, the character is neutral.
Your faction will be defaulted to friendly unless you specifically override it.