circle-ir-ai 2.22.0 → 2.27.0

package/dist/cluster/cluster.js

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+/**
+ * Cluster Layer — Foundation
+ *
+ * Top-of-pipeline file clustering (cognium-ai#154, P4 of epic #155).
+ * Groups files in a repo by their static structural fingerprint (CK
+ * metrics + import/annotation set) so downstream passes can apply
+ * per-cluster policy bundles ("library bootstrap" vs "controller
+ * surface" vs "data-access shim") instead of one-size-fits-all
+ * discovery/verification.
+ *
+ * This file ships the **foundation only**:
+ *   - `extractClusterVector(circleIr)` — pull CK vector from analyze() output
+ *   - `clusterFiles(inputs)` — deterministic k-medoids, returns
+ *     `Map<filePath, clusterId>` per acceptance #1
+ *   - distance functions (Euclidean on normalized CK + Jaccard on
+ *     imports/annotations) + the k-medoids loop itself
+ *   - `ClusterPolicy` type so downstream wiring can land in a
+ *     follow-up without re-declaring shape
+ *
+ * **Explicitly out of scope here** (tracked as follow-up tickets):
+ *   - `meta.json.files[*].clusterId` field — needs scan-emit schema
+ *     migration (Acceptance #3)
+ *   - top-100 HIGH/CRIT reduction validation (Acceptance #4)
+ *   - CWE-Bench-Java regression check (Acceptance #5)
+ *   - `--cluster-policy <profile>` CLI flag in cognium-ai
+ *     (Acceptance #6)
+ *   - LLM cluster labeling pass (optional future per the issue)
+ *
+ * The split is deliberate: P1-P3 of epic #155 were single-shot
+ * cache wins; P4's policy bundles + the two benchmark validation
+ * gates need empirical tuning that can't complete in a single
+ * release cycle. Foundation-first lets cognium-ai start consuming
+ * `clusterFiles()` as an opaque grouping signal while the policy
+ * resolver is iterated separately.
+ *
+ * **Determinism:** k-medoids is seeded from a digest of (sorted
+ * file paths || vector signature) so re-runs on the same input
+ * produce the same cluster assignments. Tie-breaking on equal
+ * distances falls back to lexicographic path order.
+ */
+import * as crypto from 'crypto';
+export const DEFAULT_CLUSTER_POLICY = {
+    contextProfile: 'application',
+    sourceWhitelist: [],
+    sinkWhitelist: [],
+    llmEnabled: true,
+};
+// ───────────────────────────────────────────────────────────────────
+// CK vector extraction
+// ───────────────────────────────────────────────────────────────────
+/**
+ * Names emitted by circle-ir's CK metric passes. Mirrored from
+ * the JSDoc on `MetricValue` in circle-ir's public type surface
+ * (canonical: "CBO" | "RFC" | "LCOM" | "DIT" | "NOC" | "WMC").
+ * Matching is case-insensitive because metric-pass authors have
+ * historically used both casings.
+ */
+const CK_METRIC_KEYS = ['CBO', 'RFC', 'LCOM', 'DIT', 'NOC', 'WMC'];
+function findMetric(metrics, name) {
+    if (!metrics)
+        return 0;
+    const lower = name.toLowerCase();
+    const hit = metrics.find((m) => m.name.toLowerCase() === lower);
+    return hit ? hit.value : 0;
+}
+/**
+ * Extract a ClusterVector from a single-file `CircleIR` analyze()
+ * result. Missing metrics default to 0 — the cluster vector is
+ * structural, so a procedural file with no CK numbers will land
+ * in the "low-complexity" cluster naturally (it's a valid signal,
+ * not missing data).
+ */
+export function extractClusterVector(circleIr) {
+    const metrics = circleIr.metrics?.metrics;
+    // Import package signatures — keep top-2 segments (e.g.
+    // `java.util.List` → `java.util`) so unrelated imports of
+    // different leaf types in the same package don't artificially
+    // increase Jaccard distance. circle-ir's `ImportInfo` carries
+    // `from_package` (the canonical package path) and falls back to
+    // `imported_name` when `from_package` is null (wildcard / default
+    // imports).
+    const imports = Array.from(new Set((circleIr.imports ?? [])
+        .map((imp) => {
+        const raw = imp.from_package ?? imp.imported_name ?? '';
+        const parts = raw.split('.');
+        return parts.length >= 2 ? parts.slice(0, 2).join('.') : raw;
+    })
+        .filter((s) => s.length > 0)));
+    // Class-level annotations (Java: `@RestController`, `@Service`,
+    // `@Entity`; Python: `@app.route` would surface here if circle-ir
+    // attaches it to the class node). Pulled from `types[*].annotations`.
+    const annotations = Array.from(new Set((circleIr.types ?? [])
+        .flatMap((t) => t.annotations ?? [])
+        .filter((s) => typeof s === 'string' && s.length > 0)));
+    // Public surface = count of types + methods that aren't explicitly
+    // marked private. `TypeInfo` has no visibility field in circle-ir's
+    // surface (all top-level types count as "public-ish" for clustering
+    // purposes); methods carry `modifiers: string[]` from which we pull
+    // the visibility token.
+    let publicSurface = 0;
+    for (const t of circleIr.types ?? []) {
+        publicSurface++;
+        for (const m of t.methods ?? []) {
+            if (!(m.modifiers ?? []).includes('private'))
+                publicSurface++;
+        }
+    }
+    return {
+        cbo: findMetric(metrics, 'CBO'),
+        rfc: findMetric(metrics, 'RFC'),
+        lcom: findMetric(metrics, 'LCOM'),
+        dit: findMetric(metrics, 'DIT'),
+        noc: findMetric(metrics, 'NOC'),
+        wmc: findMetric(metrics, 'WMC'),
+        imports,
+        publicSurface,
+        annotations,
+    };
+}
+// ───────────────────────────────────────────────────────────────────
+// Distance functions
+// ───────────────────────────────────────────────────────────────────
+/**
+ * Per-axis max-normalize the CK + publicSurface scalars across the
+ * input set. Max-normalize (rather than z-score) is deliberate:
+ * cluster boundaries should be robust to outliers (one god-class
+ * with WMC=400 shouldn't squash everything else into the same
+ * cluster), and max-normalize gives a clean [0,1] domain that
+ * combines naturally with Jaccard.
+ *
+ * Returns the maxima so callers can normalize new vectors against
+ * the same scale (e.g. for the k-medoids loop on the same set).
+ */
+export function computeNormalization(inputs) {
+    const max = (sel) => Math.max(1, ...inputs.map((i) => sel(i.vector)));
+    return {
+        cboMax: max((v) => v.cbo),
+        rfcMax: max((v) => v.rfc),
+        lcomMax: max((v) => v.lcom),
+        ditMax: max((v) => v.dit),
+        nocMax: max((v) => v.noc),
+        wmcMax: max((v) => v.wmc),
+        publicSurfaceMax: max((v) => v.publicSurface),
+    };
+}
+/** Euclidean distance on the max-normalized CK + publicSurface scalars. */
+export function euclideanCkDistance(a, b, norm) {
+    const dx = [
+        (a.cbo - b.cbo) / norm.cboMax,
+        (a.rfc - b.rfc) / norm.rfcMax,
+        (a.lcom - b.lcom) / norm.lcomMax,
+        (a.dit - b.dit) / norm.ditMax,
+        (a.noc - b.noc) / norm.nocMax,
+        (a.wmc - b.wmc) / norm.wmcMax,
+        (a.publicSurface - b.publicSurface) / norm.publicSurfaceMax,
+    ];
+    return Math.sqrt(dx.reduce((acc, x) => acc + x * x, 0));
+}
+/**
+ * Jaccard distance on two string sets (1 - |intersection|/|union|).
+ * Returns 0 when both sets are empty (semantically: nothing
+ * distinguishes them on this axis).
+ */
+export function jaccardDistance(a, b) {
+    if (a.length === 0 && b.length === 0)
+        return 0;
+    const sa = new Set(a);
+    const sb = new Set(b);
+    let intersect = 0;
+    for (const x of sa)
+        if (sb.has(x))
+            intersect++;
+    const union = sa.size + sb.size - intersect;
+    if (union === 0)
+        return 0;
+    return 1 - intersect / union;
+}
+/**
+ * Combined per-pair distance. Weights mirror the issue's signal
+ * vector ordering (CK is the primary signal; imports + annotations
+ * are tiebreakers). Total is in [0,1] so it composes cleanly with
+ * other metric-space algorithms.
+ *
+ * Weights chosen to sum to 1:
+ *   0.6 — CK + publicSurface Euclidean (clamped to 1 by sqrt of 7
+ *         normalized components, since each (a-b)/max is in [-1,1])
+ *   0.2 — imports Jaccard
+ *   0.2 — annotations Jaccard
+ *
+ * Euclidean is divided by sqrt(7) to renormalize to [0,1] before
+ * weighting — without this, the CK term can exceed 1 and the total
+ * stops being a proper [0,1] distance.
+ */
+export function mixedDistance(a, b, norm) {
+    const ck = euclideanCkDistance(a, b, norm) / Math.sqrt(7);
+    const importsD = jaccardDistance(a.imports, b.imports);
+    const annotationsD = jaccardDistance(a.annotations, b.annotations);
+    return 0.6 * ck + 0.2 * importsD + 0.2 * annotationsD;
+}
+// ───────────────────────────────────────────────────────────────────
+// Seeded PRNG (deterministic across runs)
+// ───────────────────────────────────────────────────────────────────
+/**
+ * Mulberry32 — fast, well-distributed seeded PRNG. We don't need
+ * cryptographic randomness here, just reproducibility across runs
+ * for the same input set. Seed is derived from a digest of the
+ * sorted (path || vector) signatures so adding/removing files
+ * changes the seed but reordering inputs does not.
+ */
+function mulberry32(seed) {
+    let s = seed >>> 0;
+    return () => {
+        s = (s + 0x6d2b79f5) >>> 0;
+        let t = s;
+        t = Math.imul(t ^ (t >>> 15), t | 1);
+        t ^= t + Math.imul(t ^ (t >>> 7), t | 61);
+        return ((t ^ (t >>> 14)) >>> 0) / 4294967296;
+    };
+}
+function deriveSeed(inputs) {
+    const sig = inputs
+        .map((i) => `${i.filePath}\0${i.vector.cbo},${i.vector.rfc},${i.vector.lcom},${i.vector.dit},${i.vector.noc},${i.vector.wmc},${i.vector.publicSurface}`)
+        .sort()
+        .join('|');
+    const hash = crypto.createHash('sha256').update(sig).digest();
+    return hash.readUInt32BE(0);
+}
+/**
+ * PAM-lite k-medoids on `inputs`.
+ *
+ * 1. Seed selection ("build" phase): pick the medoid that minimizes
+ *    total distance to all points, then iteratively pick the point
+ *    that maximizes minimum distance to existing medoids. This is
+ *    deterministic given the seed and degenerates gracefully when
+ *    `inputs.length <= k`.
+ * 2. Assignment: each point joins its closest medoid (lex path
+ *    tiebreak on equal distances).
+ * 3. Swap phase: for each cluster, find the point that minimizes
+ *    intra-cluster distance and promote it to medoid. Repeat until
+ *    no medoid changes (or `maxIter` hits).
+ *
+ * Complexity is O(n^2 * iter) on the distance matrix. For the
+ * top-100 sweep (n ≈ 5000 per repo at the high end) this is ~25M
+ * pairwise computations per iteration — fine for the <2s budget
+ * in Acceptance #2 because distances are scalar arithmetic on
+ * a 9-dim vector.
+ */
+export function clusterFiles(inputs, options) {
+    const k = Math.max(1, Math.min(options.k, inputs.length));
+    const maxIter = options.maxIter ?? 50;
+    if (inputs.length === 0) {
+        return { k: 0, assignments: [], medoids: [], iterations: 0 };
+    }
+    // Sort by path so ties are broken lexicographically regardless of
+    // input order.
+    const sorted = [...inputs].sort((a, b) => a.filePath.localeCompare(b.filePath));
+    const n = sorted.length;
+    const norm = computeNormalization(sorted);
+    // Precompute distance matrix (symmetric, diagonal zero).
+    const dist = Array.from({ length: n }, () => new Array(n).fill(0));
+    for (let i = 0; i < n; i++) {
+        for (let j = i + 1; j < n; j++) {
+            const d = mixedDistance(sorted[i].vector, sorted[j].vector, norm);
+            dist[i][j] = d;
+            dist[j][i] = d;
+        }
+    }
+    // Build phase — deterministic seed init.
+    const seed = options.seed ?? deriveSeed(sorted);
+    const rng = mulberry32(seed);
+    const medoidIdx = [];
+    // First medoid: minimize total distance to all points (1-medoid PAM).
+    let bestSum = Infinity;
+    let bestIdx = 0;
+    for (let i = 0; i < n; i++) {
+        let sum = 0;
+        for (let j = 0; j < n; j++)
+            sum += dist[i][j];
+        if (sum < bestSum || (sum === bestSum && sorted[i].filePath < sorted[bestIdx].filePath)) {
+            bestSum = sum;
+            bestIdx = i;
+        }
+    }
+    medoidIdx.push(bestIdx);
+    // Remaining medoids: maximize min-distance to existing medoids.
+    // RNG breaks ties on equally-far candidates for deterministic but
+    // non-degenerate seeding when the set has structural symmetry.
+    while (medoidIdx.length < k) {
+        let bestPick = -1;
+        let bestMinDist = -1;
+        const candidates = [];
+        for (let i = 0; i < n; i++) {
+            if (medoidIdx.includes(i))
+                continue;
+            let minD = Infinity;
+            for (const m of medoidIdx) {
+                if (dist[i][m] < minD)
+                    minD = dist[i][m];
+            }
+            if (minD > bestMinDist) {
+                bestMinDist = minD;
+                bestPick = i;
+                candidates.length = 0;
+                candidates.push(i);
+            }
+            else if (minD === bestMinDist) {
+                candidates.push(i);
+            }
+        }
+        if (bestPick === -1)
+            break;
+        // Tiebreak: lex-first wins; if rng() < 0.5, allow a randomized
+        // alternative from the tied set. This preserves determinism
+        // (same seed → same pick) while avoiding pathological pile-ups
+        // on highly-symmetric inputs.
+        if (candidates.length > 1 && rng() < 0.5) {
+            candidates.sort((a, b) => sorted[a].filePath.localeCompare(sorted[b].filePath));
+            bestPick = candidates[Math.floor(rng() * candidates.length)];
+        }
+        else {
+            // Default: lex-first.
+            bestPick = candidates.reduce((best, c) => (sorted[c].filePath < sorted[best].filePath ? c : best), candidates[0]);
+        }
+        medoidIdx.push(bestPick);
+    }
+    // Iterate: assign → swap → check convergence.
+    let assignment = new Array(n).fill(0);
+    let iterations = 0;
+    for (let iter = 0; iter < maxIter; iter++) {
+        iterations = iter + 1;
+        // Assign each point to closest medoid (lex tiebreak via medoid order).
+        for (let i = 0; i < n; i++) {
+            let bestC = 0;
+            let bestD = dist[i][medoidIdx[0]];
+            for (let c = 1; c < medoidIdx.length; c++) {
+                const d = dist[i][medoidIdx[c]];
+                if (d < bestD ||
+                    (d === bestD && sorted[medoidIdx[c]].filePath < sorted[medoidIdx[bestC]].filePath)) {
+                    bestD = d;
+                    bestC = c;
+                }
+            }
+            assignment[i] = bestC;
+        }
+        // Swap: for each cluster, find the point that minimizes
+        // intra-cluster distance and promote it.
+        const newMedoids = [...medoidIdx];
+        for (let c = 0; c < medoidIdx.length; c++) {
+            const members = [];
+            for (let i = 0; i < n; i++)
+                if (assignment[i] === c)
+                    members.push(i);
+            if (members.length === 0)
+                continue;
+            let bestM = newMedoids[c];
+            let bestCost = Infinity;
+            for (const m of members) {
+                let cost = 0;
+                for (const other of members)
+                    cost += dist[m][other];
+                if (cost < bestCost || (cost === bestCost && sorted[m].filePath < sorted[bestM].filePath)) {
+                    bestCost = cost;
+                    bestM = m;
+                }
+            }
+            newMedoids[c] = bestM;
+        }
+        // Check convergence (medoid set stable).
+        let changed = false;
+        for (let c = 0; c < newMedoids.length; c++) {
+            if (newMedoids[c] !== medoidIdx[c]) {
+                changed = true;
+                break;
+            }
+        }
+        medoidIdx.length = 0;
+        medoidIdx.push(...newMedoids);
+        if (!changed)
+            break;
+    }
+    const assignments = sorted.map((inp, i) => ({
+        filePath: inp.filePath,
+        clusterId: assignment[i],
+    }));
+    return {
+        k: medoidIdx.length,
+        assignments,
+        medoids: medoidIdx.map((i) => sorted[i].filePath),
+        iterations,
+    };
+}
+//# sourceMappingURL=cluster.js.map

package/dist/cluster/cluster.js.map

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package/dist/cluster/index.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Cluster layer public surface.
+ *
+ * Foundation only (cognium-ai#154, P4 of epic #155). Re-exports the
+ * primitives that downstream wiring tickets (meta.json schema, CLI
+ * flag, benchmark validation) will consume — see `cluster.ts`
+ * file-header for the scope split.
+ */
+export { clusterFiles, extractClusterVector, computeNormalization, euclideanCkDistance, jaccardDistance, mixedDistance, DEFAULT_CLUSTER_POLICY, } from './cluster.js';
+export type { ClusterVector, ClusterInput, ClusterAssignment, ClusterResult, ClusterPolicy, ContextProfile, } from './cluster.js';
+//# sourceMappingURL=index.d.ts.map

package/dist/cluster/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/cluster/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EACL,YAAY,EACZ,oBAAoB,EACpB,oBAAoB,EACpB,mBAAmB,EACnB,eAAe,EACf,aAAa,EACb,sBAAsB,GACvB,MAAM,cAAc,CAAC;AAEtB,YAAY,EACV,aAAa,EACb,YAAY,EACZ,iBAAiB,EACjB,aAAa,EACb,aAAa,EACb,cAAc,GACf,MAAM,cAAc,CAAC"}

package/dist/cluster/index.js

@@ -0,0 +1,10 @@
+/**
+ * Cluster layer public surface.
+ *
+ * Foundation only (cognium-ai#154, P4 of epic #155). Re-exports the
+ * primitives that downstream wiring tickets (meta.json schema, CLI
+ * flag, benchmark validation) will consume — see `cluster.ts`
+ * file-header for the scope split.
+ */
+export { clusterFiles, extractClusterVector, computeNormalization, euclideanCkDistance, jaccardDistance, mixedDistance, DEFAULT_CLUSTER_POLICY, } from './cluster.js';
+//# sourceMappingURL=index.js.map

package/dist/cluster/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/cluster/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EACL,YAAY,EACZ,oBAAoB,EACpB,oBAAoB,EACpB,mBAAmB,EACnB,eAAe,EACf,aAAa,EACb,sBAAsB,GACvB,MAAM,cAAc,CAAC"}

package/dist/index.d.ts

@@ -55,4 +55,5 @@ export { analyzeComponents, enrichComponent, enrichComponents, clusterComponents
 export { summarizeFunction, summarizeAllFunctions, summarizeModule, detectRole, type FunctionEffect, type SideEffect, type SideEffectKind, type ModuleSummary, type ModuleRole, type UnderstandOptions, type UnderstandResult, } from './understand/index.js';
 export { analyzeSpecGap, parseSpecMd, type SpecGapResult, type SpecGapOptions, type RequirementMatch, type UncoveredRequirement, type UndocumentedBehavior, } from './spec-gap/index.js';
 export { loadCogniumConfig, convertCogniumConfigToPassOptions, type CogniumConfig, type Suppression, } from './config/cognium-config.js';
+export { clusterFiles, extractClusterVector, computeNormalization, euclideanCkDistance, jaccardDistance, mixedDistance, DEFAULT_CLUSTER_POLICY, type ClusterVector, type ClusterInput, type ClusterAssignment, type ClusterResult, type ClusterPolicy, type ContextProfile, } from './cluster/index.js';
 //# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAGH,cAAc,WAAW,CAAC;AAG1B,OAAO,EAAE,yBAAyB,EAAE,qBAAqB,EAAE,MAAM,0BAA0B,CAAC;AAG5F,OAAO,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAG5D,OAAO,EACL,sBAAsB,EACtB,SAAS,EACT,gBAAgB,EAChB,KAAK,SAAS,IAAI,mBAAmB,GACtC,MAAM,yBAAyB,CAAC;AAGjC,OAAO,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAC;AAGrE,OAAO,EACL,WAAW,EACX,cAAc,EACd,KAAK,OAAO,GACb,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,mBAAmB,EACnB,iBAAiB,EACjB,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,iBAAiB,CAAC;AAGzB,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,UAAU,EACV,KAAK,gBAAgB,EACrB,KAAK,wBAAwB,EAC7B,KAAK,gBAAgB,EACrB,KAAK,cAAc,EACnB,KAAK,qBAAqB,GAC3B,MAAM,qBAAqB,CAAC;AAG7B,OAAO,EACL,kBAAkB,EAClB,qBAAqB,EACrB,eAAe,EACf,mBAAmB,EACnB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACxB,KAAK,cAAc,GACpB,MAAM,uBAAuB,CAAC;AAG/B,OAAO,EACL,iBAAiB,EACjB,uBAAuB,EACvB,KAAK,YAAY,EACjB,KAAK,WAAW,EAChB,KAAK,UAAU,EACf,KAAK,SAAS,IAAI,cAAc,GACjC,MAAM,0BAA0B,CAAC;AAGlC,OAAO,EACL,WAAW,EACX,iBAAiB,EACjB,KAAK,aAAa,EAClB,KAAK,cAAc,GACpB,MAAM,6BAA6B,CAAC;AAGrC,OAAO,EACL,eAAe,EACf,cAAc,EACd,aAAa,EACb,SAAS,EACT,gBAAgB,EAChB,iBAAiB,EACjB,KAAK,WAAW,EAChB,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,KAAK,QAAQ,EACb,KAAK,WAAW,EAChB,KAAK,YAAY,EACjB,KAAK,WAAW,EAChB,KAAK,UAAU,IAAI,kBAAkB,GACtC,MAAM,0BAA0B,CAAC;AAElC,OAAO,EACL,eAAe,EACf,uBAAuB,EACvB,sBAAsB,EACtB,2BAA2B,EAC3B,KAAK,aAAa,EAClB,KAAK,YAAY,GAClB,MAAM,kCAAkC,CAAC;AAE1C,OAAO,EACL,YAAY,EACZ,eAAe,EACf,SAAS,EACT,KAAK,SAAS,EACd,KAAK,UAAU,EACf,KAAK,eAAe,EACpB,KAAK,YAAY,GAClB,MAAM,kCAAkC,CAAC;AAG1C,OAAO,EACL,gBAAgB,EAChB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,EACpB,KAAK,eAAe,EACpB,KAAK,iBAAiB,EACtB,KAAK,cAAc,EACnB,KAAK,UAAU,EACf,KAAK,YAAY,EACjB,KAAK,eAAe,EACpB,KAAK,aAAa,GACnB,MAAM,sBAAsB,CAAC;AAG9B,OAAO,EACL,aAAa,EACb,cAAc,EACd,eAAe,EACf,kBAAkB,EAClB,eAAe,EACf,gBAAgB,EAChB,qBAAqB,EACrB,qBAAqB,EACrB,oBAAoB,EACpB,KAAK,aAAa,EAClB,KAAK,cAAc,EACnB,KAAK,iBAAiB,EACtB,KAAK,YAAY,IAAI,kBAAkB,EACvC,KAAK,cAAc,EACnB,KAAK,gBAAgB,GACtB,MAAM,wBAAwB,CAAC;AAGhC,OAAO,EACL,qBAAqB,EACrB,oBAAoB,EACpB,gBAAgB,EAChB,kBAAkB,EAClB,eAAe,EACf,sBAAsB,EACtB,6BAA6B,EAC7B,qBAAqB,EACrB,yBAAyB,EACzB,aAAa,EACb,aAAa,EACb,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,YAAY,EACjB,KAAK,eAAe,EACpB,KAAK,sBAAsB,EAC3B,KAAK,cAAc,EACnB,KAAK,kBAAkB,GACxB,MAAM,yBAAyB,CAAC;AAGjC,OAAO,EACL,eAAe,EACf,kBAAkB,EAClB,uBAAuB,EACvB,0BAA0B,EAC1B,KAAK,eAAe,EACpB,KAAK,uBAAuB,EAC5B,KAAK,gBAAgB,GACtB,MAAM,oBAAoB,CAAC;AAG5B,OAAO,EACL,WAAW,EACX,iBAAiB,EACjB,aAAa,EACb,kBAAkB,EAClB,gBAAgB,EAChB,wBAAwB,EACxB,aAAa,EACb,WAAW,EACX,aAAa,EACb,KAAK,UAAU,EACf,KAAK,YAAY,EACjB,KAAK,cAAc,EACnB,KAAK,WAAW,EAChB,KAAK,SAAS,EACd,KAAK,eAAe,EACpB,KAAK,YAAY,EACjB,KAAK,YAAY,EACjB,KAAK,UAAU,EACf,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,YAAY,GAClB,MAAM,yBAAyB,CAAC;AAGjC,OAAO,EACL,SAAS,EACT,gBAAgB,EAChB,kBAAkB,EAClB,KAAK,UAAU,EACf,KAAK,gBAAgB,GACtB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,mBAAmB,EACnB,sBAAsB,EACtB,wBAAwB,EACxB,KAAK,0BAA0B,GAChC,MAAM,iCAAiC,CAAC;AAGzC,OAAO,EACL,iBAAiB,EACjB,6BAA6B,EAC7B,eAAe,EACf,YAAY,EACZ,kBAAkB,EAClB,eAAe,EACf,UAAU,EACV,mBAAmB,EACnB,KAAK,gBAAgB,EACrB,KAAK,eAAe,EACpB,KAAK,YAAY,EACjB,KAAK,aAAa,EAClB,KAAK,WAAW,EAChB,KAAK,kBAAkB,EACvB,KAAK,kBAAkB,GACxB,MAAM,sBAAsB,CAAC;AAG9B,OAAO,EACL,KAAK,WAAW,EAChB,KAAK,aAAa,EAClB,KAAK,eAAe,EACpB,KAAK,aAAa,EAClB,KAAK,OAAO,EACZ,KAAK,WAAW,EAChB,KAAK,mBAAmB,EACxB,KAAK,YAAY,EACjB,KAAK,gBAAgB,EACrB,KAAK,oBAAoB,IAAI,0BAA0B,EACvD,KAAK,gBAAgB,IAAI,qBAAqB,EAC9C,KAAK,iBAAiB,GACvB,MAAM,mBAAmB,CAAC;AAE3B,OAAO,EAAE,eAAe,EAAE,mBAAmB,EAAE,0BAA0B,EAAE,MAAM,2BAA2B,CAAC;AAC7G,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAChE,OAAO,EAAE,0BAA0B,EAAE,MAAM,iCAAiC,CAAC;AAC7E,OAAO,EAAE,yBAAyB,EAAE,MAAM,gCAAgC,CAAC;AAC3E,OAAO,EAAE,qBAAqB,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAGpF,OAAO,EACL,cAAc,EACd,sBAAsB,EACtB,kBAAkB,EAClB,mBAAmB,EACnB,cAAc,EACd,KAAK,cAAc,EACnB,KAAK,SAAS,EACd,KAAK,eAAe,EACpB,KAAK,eAAe,EACpB,KAAK,oBAAoB,EACzB,KAAK,cAAc,EACnB,KAAK,kBAAkB,EACvB,KAAK,uBAAuB,GAC7B,MAAM,oBAAoB,CAAC;AAG5B,OAAO,EAAE,wBAAwB,EAAE,MAAM,kCAAkC,CAAC;AAC5E,OAAO,EAAE,KAAK,iBAAiB,EAAE,iBAAiB,EAAE,8BAA8B,EAAE,MAAM,uBAAuB,CAAC;AAGlH,OAAO,EACL,KAAK,aAAa,EAClB,KAAK,SAAS,EACd,KAAK,YAAY,EACjB,KAAK,eAAe,EACpB,KAAK,gBAAgB,EACrB,eAAe,EACf,WAAW,EACX,gBAAgB,EAChB,eAAe,EACf,oBAAoB,EACpB,KAAK,uBAAuB,EAC5B,qBAAqB,EACrB,0BAA0B,EAC1B,qBAAqB,EACrB,iBAAiB,EACjB,KAAK,wBAAwB,EAC7B,KAAK,6BAA6B,EAClC,KAAK,cAAc,EACnB,KAAK,iBAAiB,EACtB,KAAK,kBAAkB,EACvB,KAAK,gBAAgB,EACrB,sBAAsB,EACtB,KAAK,yBAAyB,EAC9B,mBAAmB,EACnB,KAAK,sBAAsB,EAC3B,0BAA0B,EAC1B,KAAK,6BAA6B,EAClC,uBAAuB,EACvB,KAAK,0BAA0B,EAC/B,wBAAwB,EACxB,KAAK,2BAA2B,EAChC,oBAAoB,EACpB,KAAK,uBAAuB,EAC5B,kBAAkB,EAClB,KAAK,qBAAqB,EAC1B,kBAAkB,EAClB,KAAK,qBAAqB,EAC1B,cAAc,EACd,KAAK,iBAAiB,EACtB,iBAAiB,EACjB,KAAK,oBAAoB,EACzB,mBAAmB,EACnB,KAAK,sBAAsB,EAC3B,kBAAkB,EAClB,KAAK,qBAAqB,EAC1B,mBAAmB,EACnB,KAAK,sBAAsB,EAC3B,gBAAgB,EAChB,KAAK,mBAAmB,EACxB,iBAAiB,EACjB,KAAK,oBAAoB,EACzB,0BAA0B,EAC1B,KAAK,6BAA6B,EAClC,qBAAqB,EACrB,KAAK,sBAAsB,EAC3B,qBAAqB,EACrB,KAAK,8BAA8B,EACnC,mBAAmB,EACnB,KA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package/dist/index.js

@@ -90,4 +90,8 @@ export { summarizeFunction, summarizeAllFunctions, summarizeModule, detectRole,
 export { analyzeSpecGap, parseSpecMd, } from './spec-gap/index.js';
 // CogniumConfig (cognium.config.json support)
 export { loadCogniumConfig, convertCogniumConfigToPassOptions, } from './config/cognium-config.js';
+// Cluster layer (cognium-ai#154, P4 of epic #155) — foundation only,
+// downstream wiring (meta.json schema, CLI flag, benchmark validation)
+// lands in follow-up tickets.
+export { clusterFiles, extractClusterVector, computeNormalization, euclideanCkDistance, jaccardDistance, mixedDistance, DEFAULT_CLUSTER_POLICY, } from './cluster/index.js';
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,sCAAsC;AACtC,cAAc,WAAW,CAAC;AAE1B,6DAA6D;AAC7D,OAAO,EAAE,yBAAyB,EAAE,qBAAqB,EAAE,MAAM,0BAA0B,CAAC;AAE5F,SAAS;AACT,OAAO,EAAE,MAAM,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AAE5D,6EAA6E;AAC7E,OAAO,EACL,sBAAsB,EACtB,SAAS,EACT,gBAAgB,GAEjB,MAAM,yBAAyB,CAAC;AAEjC,2DAA2D;AAC3D,OAAO,EAAE,kBAAkB,EAAE,MAAM,iCAAiC,CAAC;AAErE,+BAA+B;AAC/B,OAAO,EACL,WAAW,EACX,cAAc,GAEf,MAAM,oBAAoB,CAAC;AAE5B,OAAO,EACL,eAAe,EACf,gBAAgB,EAChB,mBAAmB,EACnB,iBAAiB,GAGlB,MAAM,iBAAiB,CAAC;AAEzB,aAAa;AACb,OAAO,EACL,gBAAgB,EAChB,mBAAmB,EACnB,UAAU,GAMX,MAAM,qBAAqB,CAAC;AAE7B,eAAe;AACf,OAAO,EACL,kBAAkB,EAClB,qBAAqB,EACrB,eAAe,EACf,mBAAmB,GAKpB,MAAM,uBAAuB,CAAC;AAE/B,iBAAiB;AACjB,OAAO,EACL,iBAAiB,EACjB,uBAAuB,GAKxB,MAAM,0BAA0B,CAAC;AAElC,WAAW;AACX,OAAO,EACL,WAAW,EACX,iBAAiB,GAGlB,MAAM,6BAA6B,CAAC;AAErC,gBAAgB;AAChB,OAAO,EACL,eAAe,EACf,cAAc,EACd,aAAa,EACb,SAAS,EACT,gBAAgB,EAChB,iBAAiB,GASlB,MAAM,0BAA0B,CAAC;AAElC,OAAO,EACL,eAAe,EACf,uBAAuB,EACvB,sBAAsB,EACtB,2BAA2B,GAG5B,MAAM,kCAAkC,CAAC;AAE1C,OAAO,EACL,YAAY,EACZ,eAAe,EACf,SAAS,GAKV,MAAM,kCAAkC,CAAC;AAE1C,sBAAsB;AACtB,OAAO,EACL,gBAAgB,EAChB,cAAc,EACd,kBAAkB,EAClB,oBAAoB,GAQrB,MAAM,sBAAsB,CAAC;AAE9B,kBAAkB;AAClB,OAAO,EACL,aAAa,EACb,cAAc,EACd,eAAe,EACf,kBAAkB,EAClB,eAAe,EACf,gBAAgB,EAChB,qBAAqB,EACrB,qBAAqB,EACrB,oBAAoB,GAOrB,MAAM,wBAAwB,CAAC;AAEhC,eAAe;AACf,OAAO,EACL,qBAAqB,EACrB,oBAAoB,EACpB,gBAAgB,EAChB,kBAAkB,EAClB,eAAe,EACf,sBAAsB,EACtB,6BAA6B,EAC7B,qBAAqB,EACrB,yBAAyB,EACzB,aAAa,EACb,aAAa,GASd,MAAM,yBAAyB,CAAC;AAEjC,iCAAiC;AACjC,OAAO,EACL,eAAe,EACf,kBAAkB,EAClB,uBAAuB,EACvB,0BAA0B,GAI3B,MAAM,oBAAoB,CAAC;AAE5B,eAAe;AACf,OAAO,EACL,WAAW,EACX,iBAAiB,EACjB,aAAa,EACb,kBAAkB,EAClB,gBAAgB,EAChB,wBAAwB,EACxB,aAAa,EACb,WAAW,EACX,aAAa,GAcd,MAAM,yBAAyB,CAAC;AAEjC,6BAA6B;AAC7B,OAAO,EACL,SAAS,EACT,gBAAgB,EAChB,kBAAkB,GAGnB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,mBAAmB,EACnB,sBAAsB,EACtB,wBAAwB,GAEzB,MAAM,iCAAiC,CAAC;AAEzC,uBAAuB;AACvB,OAAO,EACL,iBAAiB,EACjB,6BAA6B,EAC7B,eAAe,EACf,YAAY,EACZ,kBAAkB,EAClB,eAAe,EACf,UAAU,EACV,mBAAmB,GAQpB,MAAM,sBAAsB,CAAC;AAkB9B,OAAO,EAAE,eAAe,EAAE,mBAAmB,EAAE,0BAA0B,EAAE,MAAM,2BAA2B,CAAC;AAC7G,OAAO,EAAE,kBAAkB,EAAE,MAAM,4BAA4B,CAAC;AAChE,OAAO,EAAE,0BAA0B,EAAE,MAAM,iCAAiC,CAAC;AAC7E,OAAO,EAAE,yBAAyB,EAAE,MAAM,gCAAgC,CAAC;AAC3E,OAAO,EAAE,qBAAqB,EAAE,cAAc,EAAE,MAAM,6BAA6B,CAAC;AAEpF,yBAAyB;AACzB,OAAO,EACL,cAAc,EACd,sBAAsB,EACtB,kBAAkB,EAClB,mBAAmB,EACnB,cAAc,GASf,MAAM,oBAAoB,CAAC;AAE5B,8CAA8C;AAC9C,OAAO,EAAE,wBAAwB,EAAE,MAAM,kCAAkC,CAAC;AAC5E,OAAO,EAA0B,iBAAiB,EAAE,8BAA8B,EAAE,MAAM,uBAAuB,CAAC;AAElH,cAAc;AACd,OAAO,EAML,eAAe,EACf,WAAW,EACX,gBAAgB,EAChB,eAAe,EACf,oBAAoB,EAEpB,qBAAqB,EACrB,0BAA0B,EAC1B,qBAAqB,EACrB,iBAAiB,EAOjB,sBAAsB,EAEtB,mBAAmB,EAEnB,0BAA0B,EAE1B,uBAAuB,EAEvB,wBAAwB,EAExB,oBAAoB,EAEpB,kBAAkB,EAElB,kBAAkB,EAElB,cAAc,EAEd,iBAAiB,EAEjB,mBAAmB,EAEnB,kBAAkB,EAElB,mBAAmB,EAEnB,gBAAgB,EAEhB,iBAAiB,EAEjB,0BAA0B,EAE1B,qBAAqB,EAErB,qBAAqB,EAErB,mBAAmB,EAEnB,eAAe,EAEf,iBAAiB,EAEjB,iBAAiB,EACjB,qBAAqB,EACrB,sBAAsB,EACtB,iBAAiB,EACjB,kBAAkB,EAGlB,mBAAmB,EACnB,sBAAsB,EAGtB,kBAAkB,EAClB,kBAAkB,EAClB,sBAAsB,GAEvB,MAAM,kBAAkB,CAAC;AAE1B,wEAAwE;AACxE,4EAA4E;AAC5E,gCAAgC;AAChC,OAAO,EAAE,mBAAmB,EAAE,MAAM,oCAAoC,CAAC;AACzE,OAAO,EAAE,kBAAkB,EAAE,MAAM,mCAAmC,CAAC;AACvE,OAAO,EAAE,sBAAsB,EAAE,MAAM,uCAAuC,CAAC;AAC/E,OAAO,EAAE,4BAA4B,EAAE,MAAM,8CAA8C,CAAC;AAC5F,OAAO,EAAE,eAAe,EAAE,MAAM,gCAAgC,CAAC;AACjE,OAAO,EAAE,0BAA0B,EAAE,MAAM,4CAA4C,CAAC;AACxF,OAAO,EAAE,6BAA6B,EAAE,MAAM,+CAA+C,CAAC;AAC9F,OAAO,EAAE,4BAA4B,EAAE,MAAM,8CAA8C,CAAC;AAC5F,OAAO,EAAE,yBAAyB,EAAE,MAAM,2CAA2C,CAAC;AAEtF,gBAAgB;AAChB,OAAO,EACL,qBAAqB,IAAI,eAAe,EACxC,mBAAmB,EACnB,uBAAuB,EAOvB,cAAc,EACd,mBAAmB,EACnB,oBAAoB,EACpB,6BAA6B,GAC9B,MAAM,oBAAoB,CAAC;AAE5B,iBAAiB;AACjB,OAAO,EACL,cAAc,EACd,sBAAsB,GAEvB,MAAM,yBAAyB,CAAC;AAEjC,mBAAmB;AACnB,OAAO,EACL,eAAe,EACf,aAAa,GAKd,MAAM,2BAA2B,CAAC;AAEnC,yBAAyB;AACzB,EAAE;AACF,2EAA2E;AAC3E,4EAA4E;AAC5E,sCAAsC;AACtC,OAAO,EACL,oBAAoB,EACpB,sBAAsB,EACtB,oBAAoB,EACpB,6BAA6B,IAAI,gCAAgC,EACjE,gBAAgB,GAEjB,MAAM,6BAA6B,CAAC;AAErC,yCAAyC;AACzC,OAAO,EACL,iBAAiB,EACjB,eAAe,EACf,gBAAgB,EAChB,iBAAiB,GAUlB,MAAM,uBAAuB,CAAC;AAE/B,sCAAsC;AACtC,OAAO,EACL,iBAAiB,EACjB,qBAAqB,EACrB,eAAe,EACf,UAAU,GAQX,MAAM,uBAAuB,CAAC;AAE/B,oBAAoB;AACpB,OAAO,EACL,cAAc,EACd,WAAW,GAMZ,MAAM,qBAAqB,CAAC;AAE7B,8CAA8C;AAC9C,OAAO,EACL,iBAAiB,EACjB,iCAAiC,GAGlC,MAAM,4BAA4B,CAAC;AAEpC,qEAAqE;AACrE,uEAAuE;AACvE,8BAA8B;AAC9B,OAAO,EACL,YAAY,EACZ,oBAAoB,EACpB,oBAAoB,EACpB,mBAAmB,EACnB,eAAe,EACf,aAAa,EACb,sBAAsB,GAOvB,MAAM,oBAAoB,CAAC"}

package/dist/llm/batch-classifier.js

@@ -69,7 +69,7 @@ export class BatchClassifier {
             for (const classifier of classifiers) {
                 const task = queue.add(async () => {
                     // Check cache first
-                    const cached = this.cache.get(file.content, classifier.name);
+                    const cached = await this.cache.get(file.content, classifier.name);
                     if (cached !== null) {
                         cacheHits++;
                         classifications.push({
@@ -94,7 +94,7 @@ export class BatchClassifier {
                         llmCalls++;
                         if (response) {
                             const findings = classifier.toFindings(response, file.path);
-                            this.cache.set(file.content, classifier.name, findings);
+                            await this.cache.set(file.content, classifier.name, findings);
                             classifications.push({
                                 filePath: file.path,
                                 classifier: classifier.name,

package/dist/llm/batch-classifier.js.map

@@ -1 +1 @@
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package/dist/llm/call-logger.d.ts

@@ -69,6 +69,20 @@ export interface LLMCallEntry {
      * surface skip-rate metrics without a separate side-channel.
      */
     skippedByPrefilter?: boolean;
+    /**
+     * cognium-ai#152 — set on synthetic "no-call" entries emitted when the
+     * persistent verify cache served a batch verification result, so the JSONL
+     * analyzer can surface verify-hit rate alongside discovery skip-rate.
+     */
+    verifyCacheHit?: boolean;
+    /**
+     * cognium-ai#134 — set on synthetic "no-call" entries emitted when the
+     * persistent discovery cache served a per-method discovery result, so the
+     * JSONL analyzer can surface discovery-hit rate as a standalone signal
+     * (the 500× duplication pathology from the 2026-06-27 sweep would show up
+     * as a near-100% hit rate here).
+     */
+    discoveryCacheHit?: boolean;
 }
 declare class LLMCallLogger {
     private path;
@@ -88,6 +102,28 @@ declare class LLMCallLogger {
         phase: string;
         context?: LLMCallEntry['context'];
     }): void;
+    /**
+     * cognium-ai#152 — record a synthetic "no-call" entry when the persistent
+     * verify cache served the batch result. Mirrors `logSkip()` so the
+     * analyzer can compute verify-hit rate without a separate side-channel.
+     */
+    logVerifyCacheHit(meta: {
+        signature: string;
+        phase: string;
+        model?: string;
+        context?: LLMCallEntry['context'];
+    }): void;
+    /**
+     * cognium-ai#134 — record a synthetic "no-call" entry when the persistent
+     * discovery cache served a per-method result. Mirrors `logVerifyCacheHit()`
+     * so the analyzer can compute discovery-hit rate independently.
+     */
+    logDiscoveryCacheHit(meta: {
+        signature: string;
+        phase: string;
+        model?: string;
+        context?: LLMCallEntry['context'];
+    }): void;
     /**
      * Log a per-attempt entry (cognium-ai#87). Tagged `kind:'attempt'`. Writes
      * to the same JSONL stream as `log()` so the analyzer can correlate. Also

package/dist/llm/call-logger.d.ts.map

@@ -1 +1 @@
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