Refactor WALProcedureStore and add more comments for better understanding the implementation

The implementation is complicated and lack of comments to say how it works.

/**
 * WAL implementation of the ProcedureStore.
 * @see ProcedureWALPrettyPrinter for printing content of a single WAL.
 * @see #main(String[]) to parse a directory of MasterWALProcs.
 */

I think at least we can move sub classes to separated files to make the class smaller, and add more comments to describe what is going on here.