BENTO-33. Prevent an NPE by not setting JAVA_HOME to null.

reviewer: milo, kiyan
BENTO-35. Move code out of bento-checkin and into kiji-checkin and modify upgrade script.

In better supporting user tracking, moved code out of the bento-checkin
submodule and into the kiji-checkin module so that it can be linked into other
projects. To respect user privacy, you can touch .kiji/.disable_kiji_checkin
file to disable command/checkin logging.

reviewer: kiyan, milo