A Sublime Text 2 package that includes a command which reindents your selection according to clojure guidelines
You can bind the command to a keybinding by putting a line of some sort in the user keybindings:
{ "keys": ["f12"], "command": "clojure_reindent"}
Usage:
- Select the whole file and run the command to autoindent everthing
- Select a block of code reperesenting a top-level function and run the command
Disclaimer: This package doesn't change or break the lines themselves to fix your indentation. It just puts the correct amount of indentation before each line. This isn't a tool to fix your bad structured code.