Restructure the state persistence-related code

[miloszm]

Summary

State persistence-related code has evolved with focus on performance yet its structure is lagging behind. Especially, the file store.rs has grown and it contains now a collection of loosely related objects including the Commit class as well as many standalone functions. There is a need to restructure the code so that the module and class structure is more intuitive and eases the code reading, maintaining and its further development.

Possible solution design or implementation

Move the Commit class and other objects to separate files, create structures for standalone functions, add more modules and submodules.

Additional context

This effort is a prerequisite for adding a database as a storage layer.