bugfix: do not filter ref-/target-only subdirs
bugfix: do not filter ref-/target-only subdirs

Updated comments and variable names to be more accurate.

Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara,Ensembl/ensembl-compara