Optimize Catalog checkpoint to not rewrite the whole content each time

[ray6080]

The problem

~~1. for any writes to the catalog, we need to maintain both read and write version of the whole catalog, basically duplicate the memory overhead unnecessarily.~~ 2. checkpoint of the catalog file triggers rewritten of the whole file, which is also unnecessary in almost all cases. ~~3. the two version design also exists in TablesStatistics. while they basically duplicate the same logic without sharing the same architecture.~~ 4. there is lack of built-in dependency management in our current catalog. RelGroup is also modelled as a Table, which is not the correct level of abstraction, as it should be the parent of a bunch of rel Tables. same for rdf graph.

Edit note: problem 1 and 2 are no longer true after the mvcc rework.