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That’s generally what relational databases are for. You might try LibreOffice Base or sqlite.
As for JSON, XML, and YAML files in particular, there are tools for doing one-off queries/transformations against them, like jq and yq.
But they need rectangular structure. How do they work on tree structures, like OP has asked?
Again, that wasn't the question.
The question reads like an XY problem, they describe DB functions for data structures so unless there's some specific reason they can't use a DB that's the right answer. A "spreadsheet for data structures" describes a relational database.
Relationships. You don't dump all your data in a single table. Take for instance the following sample JSON:
JSON
You'd structure that in SQL tables something like this:
Tables
dbo.users
dbo.games
dbo.favorites
dbo.platforms
The dbo.favorites table handles the many-to-many relationship between users and games; users can have as many favourite games as they want, and multiple users can have the same favourite game. The dbo.platforms handles one-to-many relationships; each record in this table represents a single release, but each game can have multiple releases on different platforms.
So the real question was, which tool to use in order to transform the JSON's tree into these tables & relations?
(hopefully you didn't just write this all up manually! :-))
There are tools out there to generate a SQL script from a JSON file that contains all the necessary DDL and DML statements to produce a database in full. I’m not familiar with any of them, though, so I can’t help there.