Remove the options for turning off exonerate and for not doing the projection to highest common coordinate system.  Recent bugfix makes these unneccesary.
Remove the options for turning off exonerate and for not doing the
projection to highest common coordinate system.  Recent bugfix makes
these unneccesary.

muffato/ensembl,at7/ensembl,james-monkeyshines/ensembl,at7/ensembl,mjg17/ensembl,mjg17/ensembl,danstaines/ensembl,danstaines/ensembl,muffato/ensembl,muffato/ensembl,james-monkeyshines/ensembl,at7/ensembl,james-monkeyshines/ensembl,Ensembl/ensembl,willmclaren/ensembl,at7/ensembl,mjg17/ensembl,Ensembl/ensembl,Ensembl/ensembl,Ensembl/ensembl,danstaines/ensembl,willmclaren/ensembl,james-monkeyshines/ensembl,muffato/ensembl,mjg17/ensembl