Let's take the question point wise:
1 since the amount of ₹20 lakh is refundable same is not required to be shown as income in this year, however if you forefeit such amount for any reason then you need to show it as income.
2 As you have received the land as a gift the year from which the cost needs to be indexed is the base year 2001-2002, because as per section 49 when a gift is received from a relative without consideration same needs to be indexed from the date when it was first purchased i.e. in your case from 2001-2002
3 you are going to give him land of 1100 sq yard i.e. 9900 sq ft and you will get flat of 18000 sq feet. So you need to find the FMV of the flat in that year to find your sale consideration and therefore your capital gain.
If we consider 1200/sq ft as FMV your capital gain would be sale price 21600000 and cost would be 29700000 so you will have a loss.
4 GST is applicable if in joint development agreement you give the land i.e. considered to developer before the construction is complete as such contract will convert into contract of construction and not contract of sale of complete flat and in such advance payment GST will be applicable on the value of consideration paid i.e. value of land given to him.
If you resell the property be it before the construction or after same shall not attract GST.
GST rate for residential property is 12% and for commercial property is 18% as far as I know.
5 If you sell your flats then its cost of acquisition would be 1200/sq ft assuming it's cost of acquisition is same as cost of construction and it will be short term capital gain i.e. 1800/sq ft - 1200/sq ft.
6. Since you are selling land in joint development agreement and getting flat in exchange as consideration you can reduce your capital gain by claiming exemption U/s 54F as per it's formula and in your case you can only claim exemption under this case as you are not receiving any consideration in form of money otherwise you could have invested amount in bonds u/s 54EC to claim exemption upto ₹50 lakh.
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