arduino boards manager configuration I installed the Arduino IDE 1.6.4, and used the "boards manager" to install the package for Arduino Due.

I am using c++11 in my project so i need to add the compiler.cpp.extra_flags=-std=gnu++11 like i did in the /Applications/Arduino.app/Contents/Java/hardware/arduino/platform.txt file (i am on MacOSX).
It seems that arduino is ignoring that file and using a configuration coming from somewhere else. 

Where is the downloaded package installed? Can it be configured?
Ok, as @IgnacioVazquez-Abrams suggested: the configuration files for the plugins can be found in the Arduino ide preferences directory. Click the menu Arduino->Preferences (under macosx) at the bottom of the window there is the clickable path of the preferences.txt file. In the same folder as that file you will find a packages folder, where the plugins are downloaded.