CDAP-943 Use Twill's latest unreleased ApplicationBundler

Twill's latest unreleased ApplicationBundler handles duplicate files, but the Twill version we're currently using doesn't. We'll use this ApplicationBundler until the next Twill release which will have the fixed ApplicationBundler.

Still need to test on cluster.
Can you open a JIRA to remove this class in 2.7 after twill-0.5.0 is released?