Solidifying thunderdome criteria and improvements to coord_check

The implementation of the stopseeker function and its application in pseudoscan should allow for a more fair downstream comparison in the thunderdome between genes with delayed stops and their alternative annotations. Removed the need to iterate through multiple alignments in coord_check by modifying some alignment scoring parameters. Also, good starts/stops in coord_check will now always be defined by their position to the reference (regardless of fix_start/stop status).