Added a (socket-based) server mode

Accepts conll dependency parses and returns json
frame-semantic parses.
better names in Semafor.java
Handle temp file creation and cleanup for Semafor server

add docs for server mode
set uberjar to run server by default
pull out Malt preprocessing into its own shell script
Add timing to runMalt.sh
Merge branch 'server'
3.0-alpha-02