The best medicine for sick fish is fresh water. For the time being, try changing 50% of the water every day. Physically I don't see much of anything wrong with him other than being thin. I think this is either a water issue or a tank setup issue, possibly both.
I don't want to insult your fish store employee, but I've heard it plenty of times how some employees give terrible advice. He/she might of said the water was fine but the ammonia might of been sky high. I suggest you buy a kit and test the water yourself.
Bettas naturally live in shallow water (less than a foot deep) that is often full of leaf litter and plants. Because they need to breath air, it is best to have a lot of taller plants/decor for them to rest/hide among so they can always be comfortable near the surface. This is doubly important for an ill betta. It is better to have a longer tank than a taller one. You need to either lower the water level or get some tall plants/decor that sits a mere half inch from the surface. The one bundle of java fern isn't going to cut it. I like my betta tanks to be full of plants.
In smaller tanks like a 2.5 the filter flow is often far to strong for long finned bettas. I image that he gets pushed around way to much when he isn't sitting near the bottom. I would try to baffle the flow as best you can. This may be part of the problem.
Lastly, he needs to eat. One way is to put him in a shallow bowl or cup, this is why I always keep the cups bettas come in, they have many uses. Frozen brine shrimp and blood worms are the best for picky bettas but pellets or flakes might work. While he's in the cup try feeding him a bit.