Hardware packages updated/installed via Boards Manager are installed to a different location. So even though you still see an Arduino AVR Boards hardware package at (install location)/hardware/arduino/avr/cores/arduino/HardwareSerial.h, that's not the package that the Arduino IDE is actually using.

The easiest way to find the active hardware package location is as follows:
Select a board from the hardware package from the Tools > Board menu
File > Examples > SPI > BarometricPressureSensor
Sketch > Show Sketch Folder
Move up folder levels until you reach the one that contains boards.txt

You will then find HardwareSerial.h in the cores/arduino subfolder.