I read a lot of code these days where people seem to think that descriptive variable and function names replace the need for any comments. But, even the most well written code is only going to make it clear _what_ the code it doing. The _why_ is likely to remain obscure. And without knowing why the code does what it does, it will often be impossible to know whether you can make certain changes.
//window.update; is not used because of API bug #12345 see: bugs.mysql.com/12345 so use xyz instead.
Nine times out of ten I can read and understand good code with little effort, but code often starts out looking clean and becomes messy for a reason.
The why might remain obscure, but that depends on two very important things: your documentation, as you noted; and your data structures.
Show me your flow charts and conceal your tables and I shall continue to be mystified, show me your tables and I won't usually need your flow charts; they'll be obvious. - Fred Brooks
As much as you can organize your data to make the purpose of it obvious, do that. It will make the system far easier for a new-comer to comprehend, and will make far more obvious to do you the sort of code you need to write to make the wheels turn. Where that is not enough, then use comments, but don't assume that prose is an adequate replacement for precise and logical data representation. Often times, I've found that the latter is a far better choice.