Allowing backups to go to a directory other than our current working directory. Can cause some issues with disk quotas

does not store density feature with value of 0

updated the $option in repeat coverage case . Repeat coverage script now use "-pattern" to find a database instead of -d.

no clone coordinate system in mouse exists in the new assembly, don't project to clone for mouse either

Fixed an inappropriate method of getting species aliases and changed a couple of lines to be more direct.

First draft of revised projections. Exclusions in place for inappropriate mammalian traits on birds and reptiles. Also platypus.

Awaiting GOA full blacklist of undesirable projections.

Removed fish from GO terms projections. Also double-checked order of execution code and added some explanatory comments.