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alderpath merged 1 commit into from
May 29, 2026
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Update docs for co-change, anomaly, incomplete modes #8

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5 changes: 5 additions & 0 deletions README.md
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Expand Up @@ -183,6 +183,8 @@ Quale provides structural context that helps agents make better decisions about
quale o # Orient: repo map + landmarks
quale ec --files <file> # Edit context: risk + verification candidates
quale vp --files <file> # Verify packet: co-change signal
quale risk --mode co-change # Co-change prediction: what else to read
quale verify --mode incomplete --files <file> # Detects if a change is incomplete
```

**What agents get**:
Expand Down Expand Up @@ -215,6 +217,9 @@ See [docs/EFFECT_HARNESS.md](docs/EFFECT_HARNESS.md) for full methodology.
| `quale ci check <base> <head>` | Runs structural gates, exits 0-7 with bitmask |
| `quale ci comment <base> <head>` | Posts structural report as GitHub PR comment |
| `quale ci trend` | Tracks CI metric trends over time |
| `quale risk --mode co-change` | Co-change prediction: what files change together (PMI × git) |
| `quale risk --mode anomaly` | Finds identifiers with unusually high PMI (hidden coupling) |
| `quale verify --mode incomplete` | Detects files missing from a change set (incomplete PRs) |

### Advanced primitives

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3 changes: 3 additions & 0 deletions docs/COMMANDS.md
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Expand Up @@ -77,11 +77,14 @@ These replace multiple old commands with single, mode-switched interfaces.
quale risk # Hub + capillary + vulnerability intersection
quale risk --mode hub # Hub risk only
quale risk --mode capillary # Capillary risk only
quale risk --mode co-change # Co-change prediction: PMI × git history (agent workflow)
quale risk --mode anomaly # PMI outlier detection: identifier pairs with unusual coupling

quale verify --files src/auth.ts # Combined verification: mc, scope, packet
quale verify --mode mc # Pre-edit multi-choice verification (75% accuracy)
quale verify --mode packet # Post-edit co-change signal (80% accuracy)
quale verify --mode scope # Post-edit scope verification (83% accuracy)
quale verify --mode incomplete # Incomplete change detection: flags missing co-change partners

quale health # Structural health dashboard
quale health --mode score # Single health score
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4 changes: 2 additions & 2 deletions docs/FEATURE_MATRIX.md
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Expand Up @@ -18,8 +18,8 @@ These replace multiple old commands with single, mode-switched interfaces.

| Command | Replaces | Description |
|---------|----------|-------------|
| `quale risk` | `hub-risk`, `capillary`, `vulnerability-map`, `traffic-control` | Surface risky files: hub, capillary, and their intersection. Modes: `--mode full` (default), `hub`, `capillary` |
| `quale verify` | `verify-packet`, `verify-scope`, `verify-classify`, `verify-bonds`, `verify-drift`, `guard` | Verification pipeline. Modes: `--mode full` (default), `mc`, `scope`, `packet` |
| `quale risk` | `hub-risk`, `capillary`, `vulnerability-map`, `traffic-control` | Surface risky files: hub, capillary, and their intersection. Modes: `--mode full` (default), `hub`, `capillary`, `co-change` (PMI × git prediction), `anomaly` (PMI outlier detection) |
| `quale verify` | `verify-packet`, `verify-scope`, `verify-classify`, `verify-bonds`, `verify-drift`, `guard` | Verification pipeline. Modes: `--mode full` (default), `mc`, `scope`, `packet`, `incomplete` (flags missing co-change partners) |
| `quale health` | `health-score`, `drift-check`, `parity-bit` | Structural health dashboard. Modes: `--mode dashboard` (default), `score` |
| `quale audit` | `ci-report`, `pr-report`, `check-diff`, `check-pr` | Review a diff: structural, CI, and PR reports in one command |
| `quale temporal` | `decay`, `vocabulary-trend`, `origins` | Temporal analysis: decay, vocabulary trends, and phrase lifecycles |
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