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What is the most efficient way of organizing PHP code for a CRUD application? What are the well-known naming conventions?
I have a class and its getters and setters just seem to be SQL queries. Is this correct, or how am I supposed to organize it?
You should have a look at DomainModels and DataMappers. In general, I recommend the Zend Framework and its Quickstart Tutorial, as it teaches these two very relevant patterns in a few minutes by example. You do not need to switch to Zend Framework afterwards, but it is good learning material.