Remove some foreach( ).
Finish removing foreach( ).
Fix problem with add_unique( ).
Rename masks to new_masks.
Initialize old_masks to empty.
Rename old_masks to masks.
Rename partitions to split in variable names.
Rename sub_ to partial_

e.g. sub_partitions now become partial_splits
Rename variables in match( ).
Sanitize.
Reorganize a bit.
Sanitize.
Use new function add_unique( ).
Sanitize.
Update notes.
Merge branch 'master' of github.com:bredelings/BAli-Phy