Read ontoindex-navigation first.

Refactoring with OntoIndex

1. Check impact({action: 'symbol', repo: '<repo>', target: '<symbol>', direction: 'upstream'}) before editing to map callers.
2. Run gn_safe_edit_check({repo: '<repo>', symbol: '<symbol>', intent: 'modify-body'}) before making the change; use intent: 'rename' for a rename.
3. For a rename, preview candidates with refactor({action: 'rename', repo: '<repo>', target: '<symbol>', new_name: '<new>', dry_run: true}). This is preview only (applied: false). Review every candidate, then edit the files directly. Graph edits are candidates that need review; dynamic references can be missed.
4. For extract, move, or modify-body operations, use gn_safe_refactor with repo and the matching intent; dryRun defaults to true. Review the preview before any apply.
5. After edits, call gn_verify_diff with explicit changedFiles and expectedFiles, then use gn_test_gap to inspect affected test evidence. Run the focused tests indicated by the change.

Pass repo explicitly to each OntoIndex call. When the index is stale or degraded, follow ontoindex-navigation and verify uncommitted source directly.