When I run the engine (UCI interface), I usually feed the last position from the game using
position fen ... command and get the best move back. The FEN encodes the possibility of the castlings, en passant moves and keeps the move count since the last piece capture or pawn move to enforce to 50-move draw rule.
How can the engine detect the 3-fold repetition and avoid it while playing the game? I've seen a few occasions when the engine is about 5-6 pawns ahead (a clear victory), but draws because it keeps repeating giving check to the opponent's king again and again.
Clarification: I DON'T program my own engine (well, I do, but this is totally unrelated to this question). In this question I use existing engine, think StockFish or Fruit or anything else you like. This existing engine is given the FEN and returns the "best" move it can think of. Sometimes this leads to a 3-fold repetition in a clearly won positions. How can I tell the StockFish, that it has already made this move before and should do better?