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This was the biggest problem I ran into so far. I have created a patch here. The call to cmd.exe is hardcoded, so it won't work on *nix until I figure out how to determine the os, or put in a few try/catch clauses.
I think this is significant. I'm fine with lein not being built in to clooj, and using it from a command line, but I think it's a problem that the officially default version of lein (the one now linked in the installation instructions) and the current version of clooj won't play nice together.
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