Small internal bugs in HOG class, UnionFind, batching and orthoXML helpers #122

Bugs in internal helpers that don't (yet) affect normal pipeline output, but are traps for upcoming changes, e.g. the fixes for #113 and the ete4 migration.

• Representative(rep, elements) mutates rep: the copy constructor shares the _subelements / _species sets of rep and then extends them with |= (_hog_class.py:249-259). Representatives of the previous level silently grow.
• HOG.find_representative calls the non-existent Representative.get_members (_hog_class.py:383): looking up a member that is not itself a representative raises AttributeError.
• HOG.__init__ default representatives=Optional[List[Representative]] is a typing object, not None (_hog_class.py:280).
• UnionFind.remove of a set's representative breaks find() for the other members (KeyError, zoo/unionfind.py:78). There are two copies of the class (zoo/unionfind.py, _utils_roothog.py:35).
• batch_roothogs: files with the same name in different subfolders overwrite each other in a batch (shutil.copy, batch_roothogs.py:45). Not reachable with the current flat rootHOG folder, but nothing guards against it.
• pairwise relations: an orthologGroup without children raises TypeError in set.union() (zoo/hog/transform.py:52).
• prepare_species_tree for a single-species rootHOG returns the root with one child instead of the species leaf (get_common_ancestor({'A'}), _utils_subhog.py:283). That such rootHOGs produce no group is intended; the tree shape is only an internal oddity.
• copy_tree discards the result of features.union(...) (_infer_subhog.py:752), so no features are copied. It works only because ete3 treats an empty set differently from an empty list in write(features=...).

Tests (strict xfail on PR #112)

• tests/test_hog_class.py::test_representative_with_elements_does_not_mutate_source
• tests/test_hog_class.py::test_find_representative_of_non_representative_member
• tests/test_unionfind.py::test_remove_root (both copies)
• tests/test_batch_roothogs.py::test_same_basename_in_subfolders_kept
• tests/test_pairwise_relations.py::TestOrthoxmlRelations::test_empty_group_has_no_pairs
• tests/test_species_tree_prep.py::test_prepare_species_tree_single_species