I don't believe it is legal to travel with an uncased and/or loaded long gun in a motor vehicle in Pa. I have never seen a pickup with a shotgun rack here. Also, there are no special gun laws for Philadelphia, but there sure are neighborhoods that I would avoid. There are plenty of places in NJ about which I could say the same thing.

In NJ, some magazines may be illegal if they are over a certain capacity and some long guns might be called illegal "assault weapons."
Possessing hollow point ammo is a crime if it is a gun that you're carrying. Of course normal New Jerseyans(sp.?) cannot carry handguns like we can in Pa.

Again, you can hunt and shoot there--I know I do, but I would buy any ammo here in Pa. or better yet, in tax-free Delaware.
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About the guy who was cuffed: I suspect you weren't told the entire story. This sounds something like a "Terry stop" and is likely lawful. However, I wasn't there...
Maybe some of the lawyers here can expand on the concept.