add option (unique) to column iterator to skip over paralogous bases.  this is disabled by default which is a major change.  we now explicitly enable for maf generation and liftover only.  this should fix bugs in some tools that need to visit every column like halAlignability
rename halAlignability to halAlignmentDepth as per Marks request
have make kill trailing halAlignability binaries to avoid future confusion that could result from fixing and renaming it at the same time
Merge remote-tracking branch 'origin/development'

Conflicts:
	api/impl/defaultColumnIterator.cpp
	api/impl/defaultColumnIterator.h