What's the best way to match a standard file into a single data structure for editing it?

[Clonk]

Many Nim library handle generic Json serialization. 
<https://github.com/treeform/jsony/> is my favorite, but if you just search for 
Json using NIm language on github you have multiple choices.

You can also use existing serialization protocol like Protobuff or messagepack 
for instance.

Finally, if you store binary / numerical buffer you can use HDF5. There is a 
great Nim library for it <https://github.com/Vindaar/nimhdf5>.