speed up the pipeline

added new script that uses a single java instance
to get dependencies from all parse trees instead
of one java instance per parse tree

in tecolote a paper was processed in

    real    4m45.729s
    user    7m38.415s
    sys 0m13.950s

now in is processed in

    real    1m35.070s
    user    2m40.389s
    sys 0m2.478s