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Setup
Install JEdit for your particular platform. Once install, launch the JEdit application. Using the top-level menu open Plugins > Plugin Manager... Switch to the Install tab and select Clojure and Clojure Shell. Click Install.
REPL
You can start a REPL with Plugins > Clojure Shell > Open Clojure Shell. In that submenu you will find other useful common commands.
Running Programs
Select Plugins > Console > Commando... In the window you can select various options for running the current open file.
Syntax Highlighting & Auto-indentation
First determine the platform dependent location of JEdit's mode files. For example, on OS X this will be ~/Library/JEdit/modes. Download Daniel Spiewak's Clojure mode file. Put this in the your modes directory. You also need to edit the catalog file in your modes directory. Make it look like the following:
You may need to restart JEdit.