Revert "Merge reference file just once during iterative abacas runs"

This reverts commit f83b46f6010e97f24a2a187ead28d30475c86198.
Revert "Bug fix"

This reverts commit a0d19c1542ebbdca9a4bbaf5b5dce83bab823706.
Revert "Keep merged union fasta file in scope for abacas"

This reverts commit 3b78875b70419a5924137f219221463983f61e96.