Some examples in `/docs/source/examples` are broken

[mmore500]

Known broken examples to fix or remove:

• bdtree_multi1.py
• bdtree_multi2.py
• bibtex_annotations1.py
• bibtex_annotations2.py
• bibtex_annotations3.py
• ds2.py
• paup_estimate_model.py
• paup_estimate_tree_ml.py
• pdm_tns1.py
• preorder_filtered_edge_iteration.py
• raxml_estimate_tree.py
• seqgen.py
• taxa_mgmt1a.py
• tree_list_add1.py