Since project.clj is a Clojure file, you could put this at the top of your project.clj file :
(def my-deps [["enlive" "1.1.3"]])
..and later on :
 :dependencies my-deps
Which means that you could even slurp an .edn file that you could edit however you want. I actually have this on the top of my build.boot (equivalent of project.clj but for boot) :
(defn slurp-deps []
  (read-string (slurp "resources/deps.edn")))
And I use it like so :
:dependencies (slurp-deps)
The rest would just be updating your map and writing it back to the same .edn file.
If you want to reload your dependencies after that have a look at this SO question.
Note : as an alternative, I know that this is the way to do things in a REPL with boot, and that it will fetch/load the dependencies :
boot.user=> (set-env! 
       #_=>   :resource-paths #{"src"}
       #_=>   :dependencies '[["enlive" "1.1.3"]])