_validate_assembly_gaps() no longer adds a GAP if it overlaps a manual feature (e.g., centromere) and a bunch of output changes.
 Added _sort_overlapping_annotations. _validate_assembly_gaps() has multiple changes to better handle missed / redundant gap annotations. wip.
Added first_base() and last_base() methods.
_validate_assembly_gaps() added code to ensure gap borders optimized. Switched to usign cluster() to find redundant GAPs. Others. WIP.
Error correct.
_validate_assembly_gaps() finalized components for border QC and removing redundancy. Fixed execution order.
_validate_assembly_gaps() added some code to better handle overlaps between GAPs and MANUAL features (e.g., Celias centromeres). Not perfect.  _validate_overlapping_features() is really where the failure lies -- it handles some but not all cases.
_validate_assembly_gaps() micro edits..