Are fluent interfaces a violation of the Command Query Separation Principle?

Yes, it is. All those methods are obviously returning something, and equally obviously they have side effects (judging from the fact that you don't do anything with the return value, yet you do bother to call them). Since the definition of CQS states that mutators should not return a value we have a clear-cut violation in our hands.

But does it matter to you that CQS is violated? If the fluent interface makes you more productive all things considered, and if you consider it a well-known pattern with equally well-known benefits and drawbacks, why should it matter that it violates principle X on paper?

It violates this principle when it changes objects but not when it only returns a new object.

var newObject = myObject
    .useRepository("Stuff")
    .withTransactionSupport()
    .retries(3)
    .logWarningsAndErrors(); 

If myObject is unchanged after this statement, everything is OK. Generally spoken, a fluent interface violates the CQS principle, if, and only if it has side effects.

However the question is, if your example does represent a query at all. Does "fluent" necessarily mean "query"? It could probably just be perceived as an action-fluent-interface where the same object is passed from one action to the next.