Trac #26630: clean generic_graph.py (part 3)

Done here:
- add parameter `vertices` to specify the mapping vertex to consecutive
integers to methods `_matrix_`, `incidence_matrix`,
`weighted_adjacency_matrix`. It can also be used from `kirchhoff_matrix`
- use it in `spanning_trees_count`, `lex_BFS`, `spectrum`,
`characteristic_polynomial`, `eigenvectors`, `eigenspaces`, etc.
- also do some cleaning in `to_dictionary`

URL: https://trac.sagemath.org/26630
Reported by: dcoudert
Ticket author(s): David Coudert
Reviewer(s): Frédéric Chapoton