Slowly it is all coming back, -I, I can recall that, from a very long time ago.
I added an arduinolibs parameter, so, that is a bit easier to add, for instance:
CXXSRC = $(ARDUINO)/HardwareSerial.cpp $(ARDUINO)/WRandom.cpp $(ARDUINOLIBS)/LCD4Bit/LCD4Bit.cpp
And I made a symbolic link to LCD4Bit.h in the sketch directory. After that I changed the avrdude config to work with my programmer. Now it works perfectly. So, command-R and command-U work, this is very nice for lots of uploads, it works very quick.