Add clojure.core qualifier to fns where missing

This is already the case in most places, but the few exceptions can cause errors if the code Cider sends is evaluated in an ns where `apply` or `require` either isn't present or is bound to something unexpected.

I created a [minimal example project](https://github.com/johnmastro/cider-name-qualification-error-example) that triggers an error when you jack in. The `:main` ns is set to `testproject.core`, which excludes `clojure.core/apply` and defines its own. The stacktrace from the resulting exception is [here](https://github.com/johnmastro/cider-name-qualification-error-example/blob/master/stacktrace.txt). (The `project.clj` is [here](https://github.com/johnmastro/cider-name-qualification-error-example/blob/master/project.clj) and `testproject.core` is [here](https://github.com/johnmastro/cider-name-qualification-error-example/blob/master/src/testproject/core.clj).)

Defining your own `apply` is admittedly rare (I came across this error while writing a toy metacircular interpreter) but I don't think there's a downside to adding the namespace qualification.