kiji-bento: BENTO-80. JAR deduplicator picks the shortest JAR path to link to.

 - Selects the JAR file to link to by shortest path length.
 - Use MD5 sums to identify duplicated JARs files.
 - Convert 2-spaces indent to 4-spaces indent.

issue: https://jira.kiji.org/browse/BENTO-80
review: https://review.kiji.org/r/1913
commit: https://github.com/kijiproject/kiji-bento/commit/d824b121f3fe88e8bdfae1863b815fadd8491150