for my personal project I need to edit every the bytes of every section in a chunk that is stored in a .mca file. I can already generate the bytes that I need for the blocks. The only problem I have is that I can't understand how to edit these type of files very easily in java.
Block in mca ( MC Anvil map ) editing in Java
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Here is an example using this Java NBT library, it provides instructions on including to your project in the README.
Hope this helps!