This is not JED file, but I think these are the equations to generate that.
Is there any kind of software for doing this ?
Yes, download Atmel WinCUPL - it will produce JED files from boolean equations
You need to use valid equations for the part, and .oe and ,clk terms are inferred on some small SPLDs
Usual Flop is a .D extension, but you can use .T if you tell CUPL to build that from a .D-FF which is inside the part. (register_select fwir)
WinCUPL can also create simulate vectors, which you can run on the original part and the programmed copy, to check they react the same.
The tricky part is getting 100% test coverage of the original part.
So...I see in the link above that the guy did the equation by connecting that to an arduino and running some code on it.
If the part is async only, (no registers) a simple memory-like scan can give 100% coverage.
If it includes registers, you need to consider the register state too.