When any file within the core library changes, "Build options changed, rebuilding all" prints and all files are unnecessarily recompiled.

I tested just now with arduino-PR-beta1.9-BUILD-22 on Linux 64 bit (Ubuntu 14.04), with Arduino/Genuino Zero Programming Port selected. I have preferences set to show verbose info while compiling. The problem seems to happen with any code, but this is the program I used just now:

void setup() {
  Serial.begin(9600);
}
void loop() {
  static int count=0;
  Serial.print("test ");
  Serial.print(count++);
  delay(100);
}

To produce the problem, I first clicked Verify. Then I run this in a terminal window:

touch ~/.arduino15/packages/arduino/hardware/samd/1.6.16/cores/arduino/Print.cpp

When I click Verify again after this command, the result is "Build options changed, rebuilding all", and all files in the core library are recompiled, even though only Print.cpp has changed.