fix: create .graph_hashes.json after init/reprocess

[HumanBean17]

Summary

• Move _init_hash_tracker() call into write_kuzu() so init and reprocess persist .graph_hashes.json after building the graph
• Remove two now-redundant _init_hash_tracker() calls from incremental fallback paths (incremental_rebuild and _fallback_to_full)

Problem

After init or reprocess, the first increment command treated all files as new because .graph_hashes.json didn't exist. This caused an unnecessary full rebuild every time.

Verification

rm -rf /tmp/check && .venv/bin/python build_ast_graph.py \
  --source-root tests/bank-chat-system \
  --kuzu-path /tmp/check/code_graph.kuzu --verbose
ls /tmp/check/.graph_hashes.json  # now exists with 130 files hashed

.venv/bin/ruff check .
.venv/bin/python -m pytest tests -v  # 741 passed, 11 skipped

Closes #297

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