YAML is a hellish language that is the worst combination between a configuration language and a programming language.
It does have Anchor nodes (nodes you can reuse) and Alias nodes (places where you reuse said nodes), but you cannot do partial edition on aliases.
MythicMobs, the plugin he's using, doesn't have an easy answer to partially inheriting skills, unless you program them in yourself.
Now, this should have all been done in pure Java in the first place, seeing the performance of his server (tickrate is unstable with 64 players ffs), but mald already suffers enough with GML, do you really think he'd be able to make anything substantial in Java?