I have a peugeot 206 allure I have clunking noise when changing from 1st to 2nd and from 2nd to 3rd but not when changing to forth or coming down the gear I have had a new gear box clutch and thrust

Worn synchromesh on the 1st and 2nd gear cluster...........New or reconditioned gearbox needed.

check the linkage on the gearbox, somethimes they come loose

In this model, the gearbox should be fitted with speed sensor, as it provides the info of vehicle speed to the instrument panel(dashboard) by means of speedometer and the total distance covered. So, does the speedometer work proberly, does the needle move correctly? If yes, you have to change the instrument panel. if the answer is no, then the speed sensor is not working, either the sensor itself or one of its wires is broken. Notice that this sensor is a hall-effect type, which means that there are 3 pins on the sensor , 1st is 12V supply, 2nd is 0V (earth) 3rd is a signal wire that transfers signal to the points I mentioned above.
goooooood luuuuuuuuuuuck

My first thought here is your drive shaft u joints, but only because I've been stranded more than once by these. The higher torque of second will definitely make a worn u-joint "clunk". with the window down listen carefully as you engage and release your clutch in 1st gear, if you here any "clunking" noise I would check your u-joints. To do this SAFELY;ie, using jack stand etc. get under your car and try to turn the drive shaft by hand with the car in gear. ANY play in the drive shaft is bad. I'm not sure if you meant you've changed your clutch and the pressure plate or you did change out you flywheel. either way whichever you did not change could definitely be warped.

It is a 5 speed manual transmission? If it is noisey in all gears except for 4th, then the problem is countershaft bearings.

its likley to be the clutch center plate cush springs are loos and the center plate is warped so wnen you try to get into gear the clutch is draging the gear box around,,,bipping the clutch stops the clutch spinning so no noise! all you can do is strip the lot down again and fine the fault and fix it

I still don't know what caused the problem, but there is no longer the need to find out as the dealer who sold me the car has accepted responsibility and is replacing the engine. Thank you.

you may have a problem with a sticking handbrake
usually what happens is one of the brake shoe linings comes off and gets stuck when the car is stopping
the noise your hearing in the brake releasing

It seems like the clutch pressure plate has given in. Best would be to replace the clutch pro-kit.( Clutch pressure plate, clutch plate and release bearing)

check cv joints.