updated expected outputs

Updated `genome-model-rnaseq-list2.out` because a model has a new build.
approved apipe-test-reference-alignment

This model just started running with GENOME_SOFTWARE_RESULT_TEST_NAME so
the alignments were regenerated for the first time in awhile.  BWA
alignments now use however many CPUs are available when submitted to LSF
so the -t option changed to 4 and that was the only diff.

diff -U0 <(samtools view -h /gscmnt/gc13001/info/model_data/2880887847/build133133153/alignments/112032366.bam) <(samtools view -h /gscmnt/gc9006/info/model_data/2880887847/build136534477/alignments/136537547.bam)
--- /dev/fd/63    2013-04-10 21:12:53.057852876 -0500
+++ /dev/fd/62    2013-04-10 21:12:53.057852876 -0500
@@ -116 +116 @@
-@PG    ID:2851949190    VN:0.5.9    CL:bwa aln -t4 -q 5; bwa sampe  -a 462
+@PG    ID:2851949190    VN:0.5.9    CL:bwa aln -t2 -q 5; bwa sampe  -a 462
revert default => example_values change

This probably needs to be backfilled on SomaticValidation processing
profiles and converted to an input to the model's workflow.
Restructure Genome/Db tree.