CORE-3929: switched from clojure.data.json to cheshire
upped dependencies and version

clojure -> 1.5.1
clojure-commons -> 1.4.1-SNAPSHOT
lein-iplant-rpm -> 1.4.1-SNAPSHOT
Added the jex.config namespace. Moved some code from core.clj into it.
Added a function to generate a path to a currently non-existant irods
config file.
Ported the JEX over to using clojure-commons.config for config file
reading and parsing.
Added support for jex.config to incoming_xforms.clj and process.clj
Cleaned up outgoing_xforms.clj.
Fixed the JEX to pop out a correct irods config.
Modified the porklock arguments to include the path to the irods config.
Fixed up the unit tests.
Added support for the -m option out the output job.
Fixed the unit tests.
CORE-4202: Added support for AVUs on analysis result files.
Update README.markdown
Added support for adding metadata to input files.
Merge branch '1.8' of github.com:iPlantCollaborativeOpenSource/JEX into 1.8
Merge branch '1.8' into dev