chore(graph_builder): remove shadowed and orphaned method definitions #1604

Split out of #1595 (reports 2 and 6b of 9) — filed by @rrodriguesNutrium, credit to them. Related to #1538.

graph_builder.py carries several shadowed method definitions, left behind when the file was split into indexing/persistence/writer.py and indexing/resolution/.

At least three independently shadowed names:

• add_file_to_graph — defined twice; the later definition wins
• _create_all_function_calls — separately shadowed by a later definition
• add_repository_to_graph — also defined twice

Plus two orphaned methods whose live equivalents now live elsewhere:

• _resolve_inheritance_link — zero call sites in src/; live equivalent is the free function at indexing/resolution/inheritance.py:9
• _create_csharp_inheritance_and_interfaces — zero call sites here; the live one is on GraphWriter (writer.py:891)

Why this is more than tidiness: the dead add_file_to_graph's item_mappings has drifted from the live one — the live list handles objects, mixins, extensions, modules and enum_members; the dead one handles none of them. Anyone reading the file top-to-bottom to learn which node types reach the graph gets a wrong answer, and nothing in the file signals which copy wins.

The reporter verified that deleting the unreachable region is behaviour-preserving (unit suite byte-identical before and after, every removed name traced to a live equivalent or zero call sites).