VW Golf won't start after installing new battery. Anti theft problem.

is it a factory alarm?

I don't recall 1997 year Golf's having a re-programmable code for the security system. The factory security system module is located behind the dash, and yes it can be easily bypassed by running a jumper wire over the heavier gauge red and red/black wires. A few ideas as to why your car doesn't start come to mind providing you have a no crank no start situation.

Perhaps the battery is defective and/or the cables terminals loose or corroded.

Your starter itself could be the culprit.

Verify the security system itself is de-activated by unlocking through the other doors, even the rear hatch.

Could also be a coincidental problem with anything else that effects starting including the ignition switch itself.

As soon as I put the battery in, the lights started flashing and the horn honking.

I think it was a factory equiped security system. I live in a rural area where car thefts are rare. Especially common bread and butter brands.

In my 95, I just put the key into the driver's door and turn to unlock.

Yes this is what usually happens. You simply need to unlock one of your doors using the key to disable the factory security system.

That works as long as coincidentally the wires to the doors haven't gone bad. I once had to open & close the rear doors 5 or 6 times to get the internally broken wires rearranged so that the car would start. The harness got replaced that weekend.

BTW, those wires from the B-pillar to the rear doors seem to be the most prone to breaking. You can pull the hose away from the pillar and examine the wires. Broken wires, well, are obvious. Any kinks or 'thin' or stretched portions are to be suspected. Sometimes you have to feel the wires to tell there's a problem. Usually an electrical check is not needed to find the bad wires. Repairing wires or replacing the harness depends on where the wires are damaged and how many are damaged.

Mark '95 Jetta GLS