matroska
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Read the Matroska specification
Since you asked about adding customs elements in the file, you might be interresed in this: https://github.com/Matroska-Org/ebml-specification/pull/181
It's losely defined, on purpose. But you can signal that the files you create contain your extended elements and a software that is aware of that may know how to interpret them (you get free versioning of your elements).
Links to the Matroska RFC draft and their GitHub repo are in the README now.