Clearly looked like to me that he was improving his lie. I get that it's a waste area and perhaps there was a local rule granting removal of loose impediments, but I really didn't see anything being moved that was larger than the sand or pebbles that consisted of the waste area as a whole.
That said, was that a rules official observing his gardening from only 5 feet away? He said nothing, gave no warning?
Vague rules lead to lots of interpretation, and create slippery slopes like this that don't serve the game well. In a similar way, the same thing happened to Dustin Johnson @ Whistling Straits way back when he grounded his club in what turned out to be a bunker, but didn't appear to be.