Update non-bukkit dependencies

Changes to update non-bukkit dependencies.  Several changes follow @ddeaguiar's as described in Issue #43.  Most changes were pretty straightforward.   Next step will be getting bukkit to a more modern 1.6.4

```
[org.clojure/clojure         "1.5.1"]
[org.clojure/tools.logging   "0.2.6"]
[org.clojure/tools.nrepl     "0.2.3"]
[clojure-complete            "0.2.3"]
[cheshire                    "5.2.0"]
```