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It seems that the default location of the .nrepl-port file is where the lein command is run. I need to override this since I don't have permission to write files in the directory I have to run. Specifically I'm running:

lein update-in :dependencies conj \[nrepl\ \"0.8.2\"\] -- update-in :plugins conj \[cider/cider-nrepl\ \"0.25.3\"\] -- repl :headless :host localhost

I browsed the source code of leiningen for .nrepl-port and saw :root is set somewhere. I tried passing that in but it didn't seem to affect anything.

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Not a nrepl expert, but with a search about "nrepl-port" in github.com/nrepl/nrepl i find this:
https://github.com/nrepl/nrepl/blob/933e08b7ef0a66002bf5bf6369088515e1c4b42f/src/clojure/nrepl/cmdline.clj#L420

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