Hi, I Am 21 Yrs Old Man. I Was Diagnosed

Hi,
I am 21 yrs old man. I was diagnosed with chondromalacia patella 3 years back in both my knees. Doctor advised me to wear knee cap and asked me to do some exercise with 0.5 kg weights tied on my leg. He advised me not to run, bend knee, and climb stairs. Last year i joined a gym and did some leg exercises like squats, cycling etc, it was uncomfortable but still i continued thinking it will strengthen my knees. Due to some reasons i left gym. I even didnt followed everything doctor had told me like i continued climbing stairs, sometimes bending my knees. But from the last 6-7 months, i didnt had much pain in my knees i.e almost negligible. So, a week back i decided to start jogging, i jog mostly 2.5-3 kms per day at a very low speed on roads, after that i do some squats and pushups. After 2 days my knee started paining, so i have stopped doing squats and now i only jog and do push ups but knee pain has increased. So,should i stop jogging. Is squats and lunges harmful for my leg. How can i treat condromalacia, kindly suggest?
P.S: I wear knee cap while jogging and doing exercises.