Pop the fragment backstack without playing the Pop-Animation

So Warpzit was on the right track, he just didn't address your specific issue too well. I came across the exact same issue and here is how I solved it.

First I created a static boolean variable (for simplicity's sake, lets put it in the FragmentUtils class)...

public class FragmentUtils {
    public static boolean sDisableFragmentAnimations = false;
}

Then, in EVERY fragment you have, you need to override the onCreateAnimation method...

@Override
public Animation onCreateAnimation(int transit, boolean enter, int nextAnim) {
    if (FragmentUtils.sDisableFragmentAnimations) {
        Animation a = new Animation() {};
        a.setDuration(0);
        return a;
    }
    return super.onCreateAnimation(transit, enter, nextAnim);
}

Then, when you need to clear the backstack from your activity simply do the following...

public void clearBackStack() {
    FragmentUtils.sDisableFragmentAnimations = true;
    getSupportFragmentManager().popBackStackImmediate(null, FragmentManager.POP_BACK_STACK_INCLUSIVE);
    FragmentUtils.sDisableFragmentAnimations = false;
}

And voila, a call to clearBackStack() will drop you back into the root fragment without any transition animations.

Hopefully the big G will add a less stupid way of doing this in the future.

So for the support library following works:

In the fragment which should have a custom pop animation you override the onCreateAnimation with your own custom one. You could get it and set some kind of parameter depending on what you want. There might need to be done some extra work to make it work with regular fragments.

Here is the example where I'm overriding it and changing the set duration:

@Override
public Animation onCreateAnimation(int transit, boolean enter, int nextAnim) {
    Animation anim = (Animation) super.onCreateAnimation(transit, enter, nextAnim);
    if(!enter) {
        if(anim != null) {
            anim.setDuration(0); // This doesn't seem to be called.
            return anim;
        } else {
            Animation test = new TestAnimation();
            test.setDuration(0);
            return test;
        }
    }
    return anim;
}

private class TestAnimation extends Animation {

}