add internal representations and row mappers into every dao class
add some abstract methods to retrieve elements with raw query
[BUG_FIX] fix a bug in get method
re-implement a function to get elements with raw queries in CloneClassDao
[BUG_FIX] make sure related code fragment ids are updated
re-implement a function to get elements with raw queries in CloneClassMappingDao
add a method to generate a query to get values of specified columns
implement a function to get elements with raw queries in CloneGenealogyDao