Simplify travis scripts; fix -runLocal for driver; use -localOutput as home for STATS, DUMP_FASTA, and PLOT_SUBGRAPH

@anbangx @Nan-Zhang @JavierJia 

Sorry to submit these three separate ideas in one PR.

 * With these changes, the `-runLocal` option should no longer stall when running the driver.  I still don't have a solution for test cases run within eclipse, where I occasionally see the tests hang.  We shouldn't see the "no output received in 10 minutes" error you see in travis right now.
 * When we separated the unit tests from the pipeline tests, we lost the actual command that was failing for pipeline tests.  Travis now prints it.
 * `STATS`, `DUMP_FASTA`, and `PLOT_SUBGRAPH` now all write to HDFS but will be copied to the local output directory if the user specifies `-localOutput`.  Their naming is also simplified to be clearer (if the last clean step had output `05-MERGE`, then these steps will be outputted as `05-MERGE-DUMP_FASTA` rather than `06-DUMP_FASTA`. That is, the basename is kept for these jobs that don't procude their own output. This should  help our testing.