kiji-express: EXP-345. Rename root and flow modules of Kiji Express

issue: https://jira.kiji.org/browse/EXP-345
review: https://review.kiji.org/r/1438
commit: https://github.com/kijiproject/kiji-express/commit/82d7ee59e2c704fca6fd9b9ffc5e6ce0110a6ecd