ontograph/ontoindex/ontoindex-refactoring

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 audit({action: "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 refactor({action: "safe_refactor", ...}) with repo and the matching intent; dryRun defaults to true. Review the preview before any apply.
5. After edits, call audit({action: "verify_diff", ...}) with explicit changedFiles and expectedFiles, then use audit({action: "test_gap", ...}) to inspect affected test evidence. Run the focused tests indicated by the change.

Pass repo explicitly to each OntoIndex call. Use stale/refreshing results with freshness labels, and verify edited or new code from source. Follow ontoindex-navigation for degraded/untrusted evidence or failed calls; staleness alone never requires grep-only fallback.