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    <p>Outputting my object files to the desired directory with $(CC) -o $@ (and removing the mv *.o commands in my target rules) solves my problem. Everything links as expected now.</p> <p>Thanks to <a href="https://stackoverflow.com/users/893/greg-hewgill">Greg</a> and <a href="https://stackoverflow.com/users/377270/sarnold">sarnold</a> who explained how to do this in the comments.</p> <p>My makefile now looks like this:</p> <pre><code>CC = clang++ CFLAGS = -Wall -O3 -flto -m64 MAKE = make RM = \rm -f TARGET-DIR = build OBJ-DIR = $(TARGET-DIR)/obj OBJS = $(addprefix $(OBJ-DIR)/, MCTS.o NodePool.o Node.o FastMath.o \ Board.o Patterns.o FastSet.o FastHash.o FastHash2.o FastHashMap.o) GTP-OBJS = $(addprefix $(OBJ-DIR)/, GtpPlayer.o) GTP-TARGET = $(TARGET-DIR)/go-gtp TEST-OBJS = $(addprefix $(OBJ-DIR)/, TestsMain.o MCTSTests.o NodePoolTests.o \ NodeTests.o FastMathTests.o BoardTests.o FastSetTests.o \ FastHashTests.o FastHash2Tests.o FastHashMapTests.o) TEST-TARGET = $(TARGET-DIR)/go-test .PHONY : all all : $(GTP-TARGET) $(TEST-TARGET) $(GTP-TARGET) : $(GTP-OBJS) $(OBJS) $(CC) $(CFLAGS) $^ -o $@ $(OBJ-DIR)/GtpPlayer.o : GtpPlayer.cpp $(CC) -c $(CFLAGS) $&lt; -o $@ $(OBJ-DIR)/%.o : mcts/%.cpp $(CC) -c $(CFLAGS) $&lt; -o $@ $(OBJ-DIR)/%.o : board/%.cpp $(CC) -c $(CFLAGS) $&lt; -o $@ $(OBJ-DIR)/%.o : struct/%.cpp $(CC) -c $(CFLAGS) $&lt; -o $@ $(TEST-TARGET) : $(TEST-OBJS) $(OBJS) $(CC) $(CFLAGS) $^ -o $@ $(OBJ-DIR)/%.o : test/%.cpp $(CC) -c $(CFLAGS) $&lt; -o $@ .PHONY : clean clean : $(RM) $(OBJ-DIR)/*.o .PHONY : distclean distclean : $(MAKE) clean $(RM) $(GTP-TARGET) $(TEST-TARGET) .PHONY : again again: $(MAKE) distclean $(MAKE) $(GTP-TARGET) $(MAKE) $(TEST-TARGET) .PHONY : tar tar: tar cfv $(GTP-TARGET).tar $(GTP-OBJS) $(OBJS) tar cfv $(TEST-TARGET).tar $(TEST-OBJS) $(OBJS) </code></pre>
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