lister for copycat annotation data
add tests for allocation file permission setting
grab allocations correctly
fix bugs
add a test
Move tmp directory creation back into loop

The temp directory/directories need to be made in the loop or the files
will not be uniquely named.
Changes to more efficiently grab the models for the entities.

Call a different optimized path based on the class of entity
we're looking up.
Updated class browser cache.
Updated `genome` tab completion.
Updated `gmt` tab completion.
set root allocation directory to read only
unset WF_USE_FLOW for testing
make version a string so test data can be designated in a clear manner
remove HqPos report from RefAlign
remove (seemingly) unused VarScan import
remove gmt capture parsing-script
header fix
Added blessed build for new rnaseq test model

Doing this before adding the model to Jenkins so we don't get a failed
first run.
GMT PhradPhrap: more explicit busy file error handling
GMT PhradPhrap: change fatal_msg to UR standard error_message