Do I need to obtain a permission to fly my drone at Manchester city?

[choo choo]

Wrong! You are correct in that they use to be recommendations. But it has been since 2016 included in the CAA Air Navigation Order article 94 and 95 See the coat or arms at the top of the page with the word 'Legislation' next to it. The Air Navigation Order 2016 and has recently been updated to include the 1km limit from airports and 120 (400ft) height limit. And yes, there's more to come, much more. You'll soon have to register your aircraft and pass an on-line competency test. And possibly you'll have to use an app each and every time you fly that will tell the authorities exactly where you are! And if you think all that is a bit draconian, then you can thank all the people that didn't stick to what were previously only recommendations for that...

The last 4 lines sums it up better than I can.