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probe-run
Run one or more dynamic-verification probes against a local ephemeral docker-compose mirror of the target system. Captures observation traces as committed artefacts at `lineage/{repo}/probe-runs/{date}-{probe_id}.yaml` and merges measured values back into `feature-flows.yaml`, `test-map.yaml`, and per-sidecar `confidence_per_field` annotations. Local-only execution per APPROACH.md section 5 rule 1
log-issue
Draft an upstream-repo GitHub issue on disk. Creates the next ISS file under issues/{repo}/ with paste-ready frontmatter + body skeleton. The actual filing into GitHub is a deliberate human action — this skill never opens a real issue.
probe-define
Generate probe-skeleton YAML files at `lineage/{repo}/probes/{P-NNN}.yaml` from `feature-flows.yaml`'s uncovered test-matrix cells. Each skeleton carries the feature_id + test_class + cross-references + a TODO-marked arrange/act/observe/assert block the maintainer fills in. Accelerates probe corpus growth — slice 4 of dynamic-verification ADR. Local-only per APPROACH.md section 5 rule 12.
enrich
Run the file-analyser subagent against one or more substrate nodes to produce per-node semantic enrichment sidecars. Resolves a path / node-id / batch spec to substrate nodes; spawns file-analyser per node; validates the resulting sidecar against the schema; updates the manifest's `enrichment` block.
navigate
Find where a feature, component, or concept lives in the ODD codebase. Uses the navigation index for O(1) lookups.
reflect-feature
Run the feature-reflector subagent (Layer 4b — top-down product-owner reflection) over one composed feature flow. Produces `lineage/{repo}/feature-reflections/detail/{F-NNN}.yaml` with a stepped-back product-owner narrative + 5-15 falsifiable user-facing hypotheses + per-hypothesis verdicts (confirmed / contradicted / partial / probe-needed) traced through the implementation chain. Contradictions
triage
Convert raw scanner findings into atomic work items in the backlog. Assigns priority, category, effort, and identifies file conflicts.
next-batch
Autonomous batch driver for the rev-2 agentic-ontology sprint. Picks the next pending theme from state/sprint-themes.yaml, spawns 5 file-analyser subagents in parallel, then 5 reducers in parallel, merges deltas, refreshes coverage, appends the investigator-log entry, commits, pushes to remote, marks the theme done. Designed to be fired by `/loop` overnight without maintainer input.
orient
Quick orientation for a new session — shows system overview, current state, and available actions.
retrieve
Run the graph-retriever subagent — intelligent, iterative retrieval over the derived graph query layer. The maintainer asks a free-form information-need question ("where is X", "what depends on Y", "which findings concern Z"); the agent constructs a strong query, runs a bounded retrieve→read→judge→refine loop (≤10 iterations) with adaptive traversal, and returns a cited answer set. Emits substrate
review
Verify a `review-ready` work item (or an entire batch) meets every acceptance criterion and every Quality Bar gate. Reject by default — each check requires cited evidence. Must run in a session distinct from the `/implement` session that produced the item.
scan
Run an audit scanner against ODD repositories. Reads scanner definition, picks unscanned items from coverage manifest, writes findings, updates navigation.