upgrade protobuf library
SQLiteUtils: fix warning
jersey2: use standard json library
upgrade slf4j and jersey overall
build.gradle: generic updates

- generalize jackson version to save on redundancy
jackson: add support for Guava objects
SystemTest: fixup junit deprecated function

More clear way of defining timeouts
Merge pull request #674 from uwescience/upgrade-libs

Upgrade libs
Merge branch 'master' into shumo_replace_trove_with_hppc

Conflicts:
	build.gradle