So natural scrolling is part of something larger called smooth scrolling
in Gnome and it's automatically enabled if it picks up on a tablet or
some other ultra-portable medium. But where does leave us mouse/pad
users --be that of desktops or laptops--  that prefer natural scrolling?
Apparently, the answer is that we're on our own because xmodmap  (or at
least natural scrolling initiated via xmodmap) is an unsupported hack
("unsupported configuration ... gnome-tweak to enable weird options").

The more I thought about this problem, the more I came closer to
realizing a few things.

1. Natural scrolling via xmodmap (and gtk+ or qt) is NOT a hack, and
less an unsupported one for that matter. How do I know this? Because I
remembered that xmodmap is an Xorg utility. We still use Xorg, after
all.

2. My .Xmodmap is indeed being picked up; I know this because I've
reassigned some keys and they're implemented properly. So, gtk+/gnome is
selectively not picking up on the reverse scrolling directive.
Therefore, what's happening here is that gtk+/Gnome is not abiding by X
protocols. In other words, gtk/Gnome is at fault here and in that sense
it IS most certainly a bug.

3. I can only assume that in their desire to cater to the ultra-portable
market Gnome devs have forgotten about xmodmap, in as far as scrolling
direction (they do have event structures and something called
GdkScrollDirection ), and hard coded directionality with their "smooth
scrolling". And this is probably the source of the bug.

Solution
Allow user intervention. This is not unheard of as “Reverse Scrolling 
Direction” under System Settings is already implemented by KDE (see 
http://imagecdn.maketecheasier.com/2011/09/naturalscrolling-kde.png).


Aside
The Ubuntu app called naturalscrolling does not work and seems to have messed 
with other key reassignments, by the way, when I tried it.

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https://bugs.launchpad.net/bugs/951123

Title:
  nautilus not natural scrolling

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