Refactor tree handling outside of yaml and json stores

[autrilla]

Since we have to allow output formats different from the input ones (i.e., input yaml, output json), it would be easier to assume sops can only encrypt trees, as the Python version does. The Go version currently does not make such assumption and lets Stores do whatever they want, but by doing this, we'd need each store to create a function to port their data to and from every other store. It's easier to only support trees.

This way, the stores will only have to know how to load the tree, and dump the tree including the sops branch or not. They don't need to take care of encrypting themselves or decrypting.

[autrilla]

Partially fixed by 2077806; JSON still missing.