Runtime files and ignore rules

LumenFlow initialization and upgrade maintain ignore entries for local runtime output, including skip-gates audit files, prep latency audits, ownership audit logs and telemetry directories. Upgrade preserves your other ignore rules and leaves existing local audit bytes in place. Running upgrade again does not rewrite an already converged ignore block.

If wu:edit finds an untracked registered runtime file in a checkout with older ignore rules, it warns and continues wherever a clean tree is required. Run pnpm lumenflow:upgrade --latest to reconcile the managed rules. The warning names paths only; it does not print audit contents.

Tracked changes to runtime files and other uncommitted changes still block edits that require a clean tree. Unknown files under .lumenflow/ also remain blocking. Save the reported source changes through your normal WU workflow before retrying. Existing notes and metadata edit exemptions continue to apply.

Lifecycle events, completion stamps, migration evidence and the integrity manifest remain source-visible evidence. Runtime ignore reconciliation keeps their existing exceptions; it does not make the whole .lumenflow/ tree local.

wu:done also recognizes untracked registered runtime output. If delivery_review fails, its gate output prints an Artifact: path such as .lumenflow/artifacts/delivery-review/<wu-id>.json. In agent mode, open the gate log named by the refusal to find this path. Keep that report for inspection; you do not need to delete or commit it before retrying, even with older ignore rules. Contextual review archives remain under the same directory, grouped by WU. A later review may replace the current report; archived contextual results keep their existing content-addressed history.

Commit your fix, run wu:prep again, refresh any required review for the new candidate, then run the exact Done command prep prints. Tracked report changes, unknown adjacent files and protected evidence still block completion, subject to Done’s existing lifecycle-event and skip-audit allowances.

Native failed or partial reviews also keep their full JSON at the absolute Delivery review failure archive: path printed in the refusal, including quiet agent mode. Archives live outside the checkout under ~/.lumenflow-recovery/<repository-key>/artifacts/delivery-review/<WU>/<sha256>.json. They retain findings, file references, criteria and metadata when the current report is replaced and when successful completion removes the worktree. Identical reports reuse one archive. Keep these records until you no longer need the failure evidence; Done does not delete them. The current-report path and JSON format remain compatible.