My alarm system stopped working. I can still lock my car using they key and it will lock the whole car which means that the vacuum pump is working, but it will no longer turns on the alarm like it use to before. I checked the fuse box but everything seems to be good in there. Any idea on what could be wrong with the alarm?

Scan the central locking module with vagcom and start from there. Check out the measuring blocks and output tests too, there's tons of useful info to be had from that module.

Check your hood switch. Mine was broken when I bought the car. The lights would flash when it locked but that was it. Once I replaced the hood switch, the car flashed the lights and honked when I locked it.

I just noticed something interesting. My car locks fine from inside and from the drivers door lock, but when i try locking it from the truck it wont lock the car, everything stay open, is there maybe a sensor in the trunk and its not detecting the trunk being closed?

edit: it use to lock just fine from the trunk aswell.

Again, VCDS. You'll have live data from all the switches and sensors so you can actually check yourself instead of guessing and relying on people who haven't ever seen your car.

what should i be looking for in VCDS? I checked central locking and it showed me Hood locked Trunk locked

Check the codes, if there's nothing go through the measuring blocks one by one to test the function of the door/hood/trunk switches. If that fails it could be a wiring issue inside the trunk, so you'd have to pull the liner and inspect the lock cylinder. I'm not too familiar with the central locking module, but if there's a way to see whether you have a lock button pressed or not, that would be a good thing to check too.