This should fix problems with overflows in pulseIn(). It may make millis() slightly less precise for clock speeds that aren't multiple of 1 million, but we don't really support those anyway.
http://code.google.com/p/arduino/issues/detail?id=675
That is, there's now a pins/ directory in a platform, which includes multiple directories, each of which has its own pins_arduino.h. The boards.txt gets a new preferences, <BOARD>.build.pins, whose values is a sub-directory of the pins/ directory (possibly with a "platform:" prefix). That sub-directory is then placed in the include path during compilation.