Golf just can’t seem to get out of the way of its own rulebook, no matter how many times they tweak it.

Luckily for Rory McIlroy, he did not suffer the indignity of a two-shot penalty that he was initially told he incurred for altering the sand in a bunker Friday during second-round play in The Northern Trust.

McIlroy had reached down into the green-side trap on the 14th hole at Liberty National in Jersey City to move what he thought was a stone, but turned out to be just sand. He called the rules official over, and after a lengthy discussion, it was determined he would be penalized two shots.

When he finished his round and before he signed his scorecard, he called in the head honcho of rules, Slugger White, who then confirmed McIlroy should not be penalized because he didn’t improve his lie or his line of play. It turned a double-bogey 5 into a par, and a 1-under 70 into a 3-under 68. It got McIlroy to 9-under for the tournament, just three shots back of Dustin Johnson’s lead.

“The reason I called someone over is I don’t want anything on my conscience, either,” McIlroy said. “I feel like I play the game with integrity and I’m comfortable saying that I didn’t improve anything. I thought it was a rock; it wasn’t. I moved my hand away, and then I was like, I don’t know if I’ve done anything wrong here.

“They got the USGA involved, rang them. They sort of went back and forth a little bit, and then, in a way, it came down to me. [They] said, ‘OK, are you comfortable telling us you didn’t improve your lie?’ And for me, I am comfortable saying that.”

On the other side of the coin, earlier in the day, Webb Simpson very clearly cracked his driver, but was not allowed to bring in a replacement. The rules official put a magnifying glass to the crack, but somehow couldn’t determine if the metal was “separated.”

“Here’s my thing: If you have to put your face on the driver to see if it’s cracked, the rule needs to be changed,” Simpson said. “You can see it.”

Speaking of rules, and amid recent talk about slow play, Bryson DeChambeau paced off a 70-yard shot in the middle of the round that made the playing of his shot take more than three minutes. According to Tour policy, a player has 40 seconds from the time it is his turn to hit his shot.

DeChambeau shot his second consecutive 68 to get to 6-under.

Emiliano Grillo missed a birdie putt on his final hole, missing the cut by a shot. As the putt lipped out, he raised his middle finger — which is sure to draw a fine from the PGA Tour.

Phil Mickelson surged with a second-round 66 to get to 4-under for the tournament and make the cut comfortably.

The cut line was 1-under, and some notables to miss the weekend were Jason Day (even), Rickie Fowler (even), Xander Schauffele (even), Matt Kuchar (1-over), Bubba Watson (3-over), and Sergio Garcia (4-over).

Chris Stroud withdrew due to a back injury after an opening-round 76.