@monoes/monograph 1.3.0 → 1.4.0

package/.monomind/registry.json

@@ -0,0 +1,6 @@
+{
+  "version": "1.0.0",
+  "generatedAt": "2026-07-07T07:38:28.425Z",
+  "totalAgents": 0,
+  "agents": []
+}

package/__tests__/staleness/git-staleness.test.ts

@@ -81,13 +81,13 @@ describe('checkStaleness', () => {
     expect(report.changedSince).toHaveLength(0);
   });
 
-  it('returns isStale: false when no commit hash has been stored', () => {
-    // No stored commit hash
+  it('returns isStale: true when no commit hash has been stored', () => {
+    // No stored commit hash → staleness unknown, treat as stale
     vi.mocked(execSync).mockReturnValue('abc1234' as any);
 
     const report = checkStaleness(db, '/fake/repo');
 
-    expect(report.isStale).toBe(false);
+    expect(report.isStale).toBe(true);
     expect(report.indexedCommit).toBeNull();
     expect(report.currentCommit).toBe('abc1234');
   });

package/dist/src/analysis/cluster-quality.d.ts

@@ -18,11 +18,11 @@ export type Edge = {
  */
 export declare function silhouetteScore(memberships: Map<string, number>, edges: Edge[]): number;
 /**
- * Compute Newman–Girvan modularity Q.
+ * Compute Newman–Girvan modularity Q using the community-level formula:
+ *   Q = Σ_c [e_c / m - (a_c / 2m)²]
+ * where e_c = intra-community edges, a_c = sum of degrees in community c, m = total edges.
  *
- * Q = (1/2m) * Σ_{ij} [A_ij - k_i*k_j/(2m)] * δ(c_i, c_j)
- *
- * where m = total edge count, k_i = degree of node i, A_ij = adjacency.
+ * O(E + N) instead of O(N²).
  * Returns a value in (-0.5, 1].
  */
 export declare function modularityScore(memberships: Map<string, number>, edges: Edge[]): number;

package/dist/src/analysis/cluster-quality.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"cluster-quality.d.ts","sourceRoot":"","sources":["../../../src/analysis/cluster-quality.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,MAAM,MAAM,IAAI,GAAG;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC;AA2D1D;;;;;;GAMG;AACH,wBAAgB,eAAe,CAC7B,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAChC,KAAK,EAAE,IAAI,EAAE,GACZ,MAAM,CAoBR;AAED;;;;;;;GAOG;AACH,wBAAgB,eAAe,CAC7B,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAChC,KAAK,EAAE,IAAI,EAAE,GACZ,MAAM,CA+BR"}

package/dist/src/analysis/cluster-quality.js

@@ -84,41 +84,38 @@ export function silhouetteScore(memberships, edges) {
     return total / memberships.size;
 }
 /**
- * Compute Newman–Girvan modularity Q.
+ * Compute Newman–Girvan modularity Q using the community-level formula:
+ *   Q = Σ_c [e_c / m - (a_c / 2m)²]
+ * where e_c = intra-community edges, a_c = sum of degrees in community c, m = total edges.
  *
- * Q = (1/2m) * Σ_{ij} [A_ij - k_i*k_j/(2m)] * δ(c_i, c_j)
- *
- * where m = total edge count, k_i = degree of node i, A_ij = adjacency.
+ * O(E + N) instead of O(N²).
  * Returns a value in (-0.5, 1].
  */
 export function modularityScore(memberships, edges) {
+    if (edges.length === 0 || memberships.size === 0)
+        return 0;
     const adj = buildAdjacency(edges);
-    // Degree map (undirected) — use adj to count undirected edges correctly
-    const degree = new Map();
-    for (const [nodeId, neighbors] of adj) {
-        degree.set(nodeId, neighbors.size);
+    const m = edges.length; // directed edges count (each undirected pair counted once in input)
+    // Sum of degrees per community and intra-community edge count
+    const communityDegreeSum = new Map();
+    const intraCommunityEdges = new Map();
+    for (const [nodeId, cid] of memberships) {
+        const deg = adj.get(nodeId)?.size ?? 0;
+        communityDegreeSum.set(cid, (communityDegreeSum.get(cid) ?? 0) + deg);
+    }
+    for (const { sourceId, targetId } of edges) {
+        const cs = memberships.get(sourceId);
+        const ct = memberships.get(targetId);
+        if (cs !== undefined && ct !== undefined && cs === ct) {
+            intraCommunityEdges.set(cs, (intraCommunityEdges.get(cs) ?? 0) + 1);
+        }
     }
-    // m_undirected: each undirected edge is counted once in adj (both directions added)
-    // so sum of degrees = 2 * m_undirected
-    const totalDegree = [...degree.values()].reduce((s, d) => s + d, 0);
-    const m = totalDegree / 2;
-    if (m === 0)
-        return 0;
     const twoM = 2 * m;
     let Q = 0;
-    const nodes = [...memberships.keys()];
-    for (let i = 0; i < nodes.length; i++) {
-        const u = nodes[i];
-        for (let j = i + 1; j < nodes.length; j++) {
-            const v = nodes[j];
-            if (memberships.get(u) !== memberships.get(v))
-                continue;
-            const aij = adj.get(u)?.has(v) ? 1 : 0;
-            const ki = degree.get(u) ?? 0;
-            const kj = degree.get(v) ?? 0;
-            Q += aij - (ki * kj) / twoM;
-        }
+    for (const [cid, degSum] of communityDegreeSum) {
+        const ec = intraCommunityEdges.get(cid) ?? 0;
+        Q += ec / m - (degSum / twoM) ** 2;
     }
-    return Q / m; // normalise by m (equivalent to 1/(2m) summed both directions)
+    return Q;
 }
 //# sourceMappingURL=cluster-quality.js.map

package/dist/src/analysis/cluster-quality.js.map

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@@ -1 +1 @@
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+{"version":3,"file":"combined.d.ts","sourceRoot":"","sources":["../../../src/analysis/combined.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD,MAAM,MAAM,YAAY,GAAG,WAAW,GAAG,aAAa,GAAG,QAAQ,CAAC;AAElE,MAAM,WAAW,eAAe;IAC9B,IAAI,CAAC,EAAE,YAAY,EAAE,CAAC;IACtB,IAAI,CAAC,EAAE,YAAY,EAAE,CAAC;CACvB;AAED,MAAM,WAAW,cAAc;IAC7B,QAAQ,EAAE,GAAG,CAAC,YAAY,CAAC,CAAC;IAC5B,KAAK,EAAE,MAAM,CAAC;CACf;AAED,wBAAgB,eAAe,CAAC,IAAI,EAAE,eAAe,GAAG,GAAG,CAAC,YAAY,CAAC,CAexE;AAID,wBAAsB,WAAW,CAC/B,EAAE,EAAE,WAAW,EACf,IAAI,EAAE,eAAe,GACpB,OAAO,CAAC,cAAc,CAAC,CAIzB"}

package/dist/src/analysis/combined.js

@@ -11,6 +11,8 @@ export function resolveAnalyses(opts) {
     }
     return result;
 }
+// monolean: stub — resolves which analyses to run but doesn't execute them.
+// Wire up when dead-code/duplication detectors are called from a unified entry point.
 export async function runCombined(db, opts) {
     const analyses = resolveAnalyses(opts);
     const ranAt = new Date().toISOString();

package/dist/src/analysis/combined.js.map

@@ -1 +1 @@
-{"version":3,"file":"combined.js","sourceRoot":"","sources":["../../../src/analysis/combined.ts"],"names":[],"mappings":"AAcA,MAAM,UAAU,eAAe,CAAC,IAAqB;IACnD,IAAI,MAAM,GAAG,IAAI,GAAG,CAAe,CAAC,WAAW,EAAE,aAAa,EAAE,QAAQ,CAAC,CAAC,CAAC;IAE3E,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YAC7B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QACtB,CAAC;IACH,CAAC;IAED,IAAI,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtC,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACnC,MAAM,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC9D,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,EAAe,EACf,IAAqB;IAErB,MAAM,QAAQ,GAAG,eAAe,CAAC,IAAI,CAAC,CAAC;IACvC,MAAM,KAAK,GAAG,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IACvC,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAC;AAC7B,CAAC"}
+{"version":3,"file":"combined.js","sourceRoot":"","sources":["../../../src/analysis/combined.ts"],"names":[],"mappings":"AAcA,MAAM,UAAU,eAAe,CAAC,IAAqB;IACnD,IAAI,MAAM,GAAG,IAAI,GAAG,CAAe,CAAC,WAAW,EAAE,aAAa,EAAE,QAAQ,CAAC,CAAC,CAAC;IAE3E,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;QACd,KAAK,MAAM,IAAI,IAAI,IAAI,CAAC,IAAI,EAAE,CAAC;YAC7B,MAAM,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QACtB,CAAC;IACH,CAAC;IAED,IAAI,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QACtC,MAAM,OAAO,GAAG,IAAI,GAAG,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACnC,MAAM,GAAG,IAAI,GAAG,CAAC,CAAC,GAAG,MAAM,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC9D,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,4EAA4E;AAC5E,sFAAsF;AACtF,MAAM,CAAC,KAAK,UAAU,WAAW,CAC/B,EAAe,EACf,IAAqB;IAErB,MAAM,QAAQ,GAAG,eAAe,CAAC,IAAI,CAAC,CAAC;IACvC,MAAM,KAAK,GAAG,IAAI,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;IACvC,OAAO,EAAE,QAAQ,EAAE,KAAK,EAAE,CAAC;AAC7B,CAAC"}

package/dist/src/analysis/targets.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"targets.d.ts","sourceRoot":"","sources":["../../../src/analysis/targets.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD,MAAM,MAAM,sBAAsB,GAC9B,uBAAuB,GACvB,yBAAyB,GACzB,iBAAiB,GACjB,gBAAgB,GAChB,yBAAyB,GACzB,qBAAqB,GACrB,iBAAiB,CAAC;AAEtB,MAAM,MAAM,cAAc,GAAG,KAAK,GAAG,QAAQ,GAAG,MAAM,CAAC;AACvD,MAAM,MAAM,gBAAgB,GAAG,MAAM,GAAG,QAAQ,GAAG,KAAK,CAAC;AAEzD,MAAM,WAAW,iBAAiB;IAChC,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,sBAAsB,CAAC;IACjC,MAAM,EAAE,cAAc,CAAC;IACvB,UAAU,EAAE,gBAAgB,CAAC;IAC7B,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,wBAAwB;IACvC,OAAO,EAAE,iBAAiB,EAAE,CAAC;IAC7B,aAAa,EAAE,MAAM,CAAC;CACvB;AAWD,wBAAgB,yBAAyB,CAAC,EAAE,EAAE,WAAW,GAAG,wBAAwB,CAwHnF;AAID,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,mBAAmB,EAAE,MAAM,CAAC;CAC7B;AAED,MAAM,WAAW,cAAc;IAC7B,kBAAkB,EAAE,MAAM,CAAC;IAC3B,gBAAgB,EAAE,gBAAgB,EAAE,CAAC;IACrC,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,mBAAmB,EAAE,kBAAkB,EAAE,CAAC;CAC3C;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,0EAA0E;IAC1E,QAAQ,EAAE,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,KAAK,MAAM,GAAG,IAAI,CAAC;CAC9D;AAED,eAAO,MAAM,qBAAqB;;;;;;CAMxB,CAAC;AAEX,uEAAuE;AACvE,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,MAAM,CAGxE;AAED,yEAAyE;AACzE,wBAAgB,qBAAqB,CAAC,OAAO,EAAE;IAC7C,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;IACvB,eAAe,EAAE,MAAM,CAAC;CACzB,GAAG,MAAM,CAWT;AAED,+FAA+F;AAC/F,wBAAgB,qBAAqB,CACnC,KAAK,EAAE,YAAY,EAAE,EACrB,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAC9B;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAM9C"}
+{"version":3,"file":"targets.d.ts","sourceRoot":"","sources":["../../../src/analysis/targets.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,WAAW,EAAE,MAAM,kBAAkB,CAAC;AAEpD,MAAM,MAAM,sBAAsB,GAC9B,uBAAuB,GACvB,yBAAyB,GACzB,iBAAiB,GACjB,gBAAgB,GAChB,yBAAyB,GACzB,qBAAqB,GACrB,iBAAiB,CAAC;AAEtB,MAAM,MAAM,cAAc,GAAG,KAAK,GAAG,QAAQ,GAAG,MAAM,CAAC;AACvD,MAAM,MAAM,gBAAgB,GAAG,MAAM,GAAG,QAAQ,GAAG,KAAK,CAAC;AAEzD,MAAM,WAAW,iBAAiB;IAChC,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,aAAa,EAAE,MAAM,CAAC;IACtB,UAAU,EAAE,MAAM,CAAC;IACnB,QAAQ,EAAE,sBAAsB,CAAC;IACjC,MAAM,EAAE,cAAc,CAAC;IACvB,UAAU,EAAE,gBAAgB,CAAC;IAC7B,QAAQ,EAAE,MAAM,EAAE,CAAC;CACpB;AAED,MAAM,WAAW,wBAAwB;IACvC,OAAO,EAAE,iBAAiB,EAAE,CAAC;IAC7B,aAAa,EAAE,MAAM,CAAC;CACvB;AAWD,wBAAgB,yBAAyB,CAAC,EAAE,EAAE,WAAW,GAAG,wBAAwB,CAuHnF;AAID,MAAM,WAAW,kBAAkB;IACjC,MAAM,EAAE,MAAM,CAAC;IACf,KAAK,EAAE,MAAM,CAAC;IACd,SAAS,EAAE,MAAM,CAAC;IAClB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,gBAAgB;IAC/B,IAAI,EAAE,MAAM,CAAC;IACb,SAAS,EAAE,MAAM,CAAC;IAClB,mBAAmB,EAAE,MAAM,CAAC;CAC7B;AAED,MAAM,WAAW,cAAc;IAC7B,kBAAkB,EAAE,MAAM,CAAC;IAC3B,gBAAgB,EAAE,gBAAgB,EAAE,CAAC;IACrC,SAAS,EAAE,MAAM,EAAE,CAAC;IACpB,mBAAmB,EAAE,kBAAkB,EAAE,CAAC;CAC3C;AAED,MAAM,WAAW,YAAY;IAC3B,IAAI,EAAE,MAAM,CAAC;IACb,WAAW,EAAE,MAAM,CAAC;IACpB,MAAM,EAAE,MAAM,CAAC;IACf,0EAA0E;IAC1E,QAAQ,EAAE,CAAC,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,KAAK,MAAM,GAAG,IAAI,CAAC;CAC9D;AAED,eAAO,MAAM,qBAAqB;;;;;;CAMxB,CAAC;AAEX,uEAAuE;AACvE,wBAAgB,eAAe,CAAC,KAAK,EAAE,MAAM,EAAE,SAAS,EAAE,MAAM,GAAG,MAAM,CAGxE;AAED,yEAAyE;AACzE,wBAAgB,qBAAqB,CAAC,OAAO,EAAE;IAC7C,YAAY,EAAE,MAAM,CAAC;IACrB,YAAY,EAAE,MAAM,CAAC;IACrB,aAAa,EAAE,MAAM,CAAC;IACtB,QAAQ,EAAE,MAAM,CAAC;IACjB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;IACvB,eAAe,EAAE,MAAM,CAAC;CACzB,GAAG,MAAM,CAWT;AAED,+FAA+F;AAC/F,wBAAgB,qBAAqB,CACnC,KAAK,EAAE,YAAY,EAAE,EACrB,OAAO,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAC9B;IAAE,IAAI,EAAE,YAAY,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,GAAG,IAAI,CAM9C"}

package/dist/src/analysis/targets.js

@@ -5,13 +5,12 @@ export function computeRefactoringTargets(db) {
       n.id,
       n.file_path,
       n.properties,
-      COUNT(DISTINCT e_in.id) as in_degree,
-      COUNT(DISTINCT e_out.id) as out_degree
+      COALESCE(d_in.cnt, 0) as in_degree,
+      COALESCE(d_out.cnt, 0) as out_degree
     FROM nodes n
-    LEFT JOIN edges e_in ON e_in.target_id = n.id
-    LEFT JOIN edges e_out ON e_out.source_id = n.id
+    LEFT JOIN (SELECT target_id, COUNT(*) AS cnt FROM edges GROUP BY target_id) d_in ON d_in.target_id = n.id
+    LEFT JOIN (SELECT source_id, COUNT(*) AS cnt FROM edges GROUP BY source_id) d_out ON d_out.source_id = n.id
     WHERE n.label = 'File' AND n.file_path IS NOT NULL
-    GROUP BY n.id
   `).all();
     if (rows.length === 0) {
         return { targets: [], totalAnalyzed: 0 };

package/dist/src/analysis/targets.js.map

@@ -1 +1 @@
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package/dist/src/export/analysis-json.js

@@ -32,7 +32,7 @@ export function buildDuplicationResultsEnvelope(results, cloneGroups, opts = {})
 }
 export function stripRootPrefix(obj, rootPrefix) {
     const json = JSON.stringify(obj);
-    const escaped = rootPrefix.replace(/[/\\]/g, s => `\\${s}`);
+    const escaped = rootPrefix.replace(/[.*+?^${}()|[\]\\]/g, '\\$&');
     return JSON.parse(json.replace(new RegExp(escaped, 'g'), ''));
 }
 //# sourceMappingURL=analysis-json.js.map

package/dist/src/export/analysis-json.js.map

@@ -1 +1 @@
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package/dist/src/export/sarif.d.ts.map

@@ -1 +1 @@
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package/dist/src/export/sarif.js

@@ -1,5 +1,16 @@
 import { createHash } from 'crypto';
-import { relative } from 'path';
+import { readFileSync } from 'fs';
+import { relative, dirname, join } from 'path';
+import { fileURLToPath } from 'url';
+const __dirname = dirname(fileURLToPath(import.meta.url));
+const PKG_VERSION = (() => {
+    try {
+        return JSON.parse(readFileSync(join(__dirname, '..', '..', 'package.json'), 'utf8')).version ?? '0.0.0';
+    }
+    catch {
+        return '0.0.0';
+    }
+})();
 const SARIF_RULES = [
     {
         id: 'monograph/god-node',
@@ -149,7 +160,7 @@ export function exportHealthSarif(findings, root) {
     return {
         $schema: 'https://raw.githubusercontent.com/oasis-tcs/sarif-spec/master/Schemata/sarif-schema-2.1.0.json',
         version: '2.1.0',
-        runs: [{ tool: { driver: { name: 'monograph-health', version: '1.0.0', rules } }, results }],
+        runs: [{ tool: { driver: { name: 'monograph-health', version: PKG_VERSION, rules } }, results }],
     };
 }
 //# sourceMappingURL=sarif.js.map

package/dist/src/export/sarif.js.map

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package/dist/src/graph/baseline.d.ts.map

@@ -1 +1 @@
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package/dist/src/graph/baseline.js

@@ -83,15 +83,19 @@ export function extractFindingsFromDb(db, projectPath) {
     }
     // God nodes (degree > 50)
     const gods = db.prepare(`
-    SELECT n.id, n.name, n.file_path, n.start_line,
-           COUNT(DISTINCT e1.id) + COUNT(DISTINCT e2.id) as degree
+    SELECT n.id, n.name, n.file_path, n.start_line, d.deg as degree
     FROM nodes n
-    LEFT JOIN edges e1 ON e1.source_id = n.id
-    LEFT JOIN edges e2 ON e2.target_id = n.id
-    GROUP BY n.id
-    HAVING degree > 50
-    ORDER BY degree DESC
-    LIMIT 100
+    JOIN (
+      SELECT node_id, SUM(cnt) AS deg FROM (
+        SELECT source_id AS node_id, COUNT(*) AS cnt FROM edges GROUP BY source_id
+        UNION ALL
+        SELECT target_id AS node_id, COUNT(*) AS cnt FROM edges GROUP BY target_id
+      ) GROUP BY node_id
+      HAVING deg > 50
+      ORDER BY deg DESC
+      LIMIT 100
+    ) d ON d.node_id = n.id
+    ORDER BY d.deg DESC
   `).all();
     for (const n of gods) {
         findings.push({
@@ -126,20 +130,25 @@ export function extractFindingsFromDb(db, projectPath) {
             fingerprint: fingerprintFinding('surprise', e.source_id, e.target_id),
         });
     }
-    // Bridge nodes: nodes whose edges span more than one community_id
-    // Use JOIN+GROUP BY instead of correlated subqueries to avoid N*2 subquery executions
+    // Bridge nodes: nodes whose edges span 2+ distinct foreign communities.
+    // Pre-aggregate cross-community counts per direction to avoid 4-way cross product.
     const bridges = db.prepare(`
-    SELECT n.id, n.name, n.file_path, n.start_line,
-           COUNT(DISTINCT CASE WHEN e_out.source_id = n.id AND n_tgt.community_id != n.community_id THEN n_tgt.community_id END) +
-           COUNT(DISTINCT CASE WHEN e_in.target_id = n.id AND n_src.community_id != n.community_id THEN n_src.community_id END) AS cross_communities
+    SELECT n.id, n.name, n.file_path, n.start_line
     FROM nodes n
-    LEFT JOIN edges e_out ON e_out.source_id = n.id
-    LEFT JOIN nodes n_tgt ON n_tgt.id = e_out.target_id AND n_tgt.community_id IS NOT NULL
-    LEFT JOIN edges e_in ON e_in.target_id = n.id
-    LEFT JOIN nodes n_src ON n_src.id = e_in.source_id AND n_src.community_id IS NOT NULL
-    WHERE n.community_id IS NOT NULL
-    GROUP BY n.id
-    HAVING cross_communities >= 2
+    JOIN (
+      SELECT node_id, COUNT(DISTINCT foreign_community) AS cross_cnt FROM (
+        SELECT e.source_id AS node_id, n2.community_id AS foreign_community
+        FROM edges e
+        JOIN nodes n1 ON n1.id = e.source_id AND n1.community_id IS NOT NULL
+        JOIN nodes n2 ON n2.id = e.target_id AND n2.community_id IS NOT NULL AND n2.community_id != n1.community_id
+        UNION ALL
+        SELECT e.target_id AS node_id, n1.community_id AS foreign_community
+        FROM edges e
+        JOIN nodes n1 ON n1.id = e.source_id AND n1.community_id IS NOT NULL
+        JOIN nodes n2 ON n2.id = e.target_id AND n2.community_id IS NOT NULL AND n1.community_id != n2.community_id
+      ) GROUP BY node_id
+      HAVING cross_cnt >= 2
+    ) b ON b.node_id = n.id
     LIMIT 100
   `).all();
     for (const n of bridges) {

package/dist/src/graph/baseline.js.map

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package/dist/src/graph/health-score.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"health-score.d.ts","sourceRoot":"","sources":["../../../src/graph/health-score.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAE3C,MAAM,WAAW,oBAAoB;IACnC,kBAAkB,EAAE,MAAM,CAAC;IAC3B,UAAU,EAAE,MAAM,CAAC;IACnB,eAAe,EAAE,MAAM,CAAC;IACxB,UAAU,EAAE,MAAM,CAAC;IACnB,eAAe,EAAE,MAAM,CAAC;IACxB,qBAAqB,EAAE,MAAM,CAAC;CAC/B;AAED,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;IACnC,SAAS,EAAE,oBAAoB,CAAC;IAChC,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAMtE;AAED,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,iBAAiB,CAmH3E;AAED;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,iBAAiB,GAAG,MAAM,CA+BnE"}
+{"version":3,"file":"health-score.d.ts","sourceRoot":"","sources":["../../../src/graph/health-score.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAE3C,MAAM,WAAW,oBAAoB;IACnC,kBAAkB,EAAE,MAAM,CAAC;IAC3B,UAAU,EAAE,MAAM,CAAC;IACnB,eAAe,EAAE,MAAM,CAAC;IACxB,UAAU,EAAE,MAAM,CAAC;IACnB,eAAe,EAAE,MAAM,CAAC;IACxB,qBAAqB,EAAE,MAAM,CAAC;CAC/B;AAED,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,MAAM,CAAC;IACd,KAAK,EAAE,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAAC;IACnC,SAAS,EAAE,oBAAoB,CAAC;IAChC,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,GAAG,CAMtE;AAED,wBAAgB,kBAAkB,CAAC,EAAE,EAAE,QAAQ,CAAC,QAAQ,GAAG,iBAAiB,CAgH3E;AAED;;;;;;GAMG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,iBAAiB,GAAG,MAAM,CA+BnE"}

package/dist/src/graph/health-score.js

@@ -14,27 +14,24 @@ export function computeHealthScore(db) {
     const totalFilesRow = db.prepare("SELECT COUNT(*) as c FROM nodes WHERE label = 'File'").get();
     const totalFiles = totalFilesRow.c;
     // ── Unreachable file nodes ────────────────────────────────────────────────
-    const unreachableRow = db.prepare("SELECT COUNT(*) as c FROM nodes WHERE label = 'File' AND properties LIKE '%\"unreachable\"%'").get();
+    const unreachableRow = db.prepare("SELECT COUNT(*) as c FROM nodes WHERE label = 'File' AND json_extract(properties, '$.unreachable') = 1").get();
     const unreachableFiles = unreachableRow.c;
     // ── Total nodes ───────────────────────────────────────────────────────────
     const totalNodesRow = db.prepare('SELECT COUNT(*) as c FROM nodes').get();
     const totalNodes = totalNodesRow.c;
     // ── p95 degree (god nodes) ────────────────────────────────────────────────
-    const degreesRows = db.prepare(`
-    SELECT source_id as node_id, COUNT(*) as deg FROM edges GROUP BY source_id
-    UNION ALL
-    SELECT target_id as node_id, COUNT(*) as deg FROM edges GROUP BY target_id
+    // Compute per-node total degree (in + out) entirely in SQL
+    const degreeRows = db.prepare(`
+    SELECT node_id, SUM(cnt) AS degree FROM (
+      SELECT source_id AS node_id, COUNT(*) AS cnt FROM edges GROUP BY source_id
+      UNION ALL
+      SELECT target_id AS node_id, COUNT(*) AS cnt FROM edges GROUP BY target_id
+    ) GROUP BY node_id ORDER BY degree ASC
   `).all();
-    // Sum degrees per node
-    const degMap = new Map();
-    for (const row of degreesRows) {
-        degMap.set(row.node_id, (degMap.get(row.node_id) ?? 0) + row.deg);
-    }
-    const degrees = [...degMap.values()].sort((a, b) => a - b);
-    const p95Index = Math.floor(degrees.length * 0.95);
-    const p95Degree = degrees[p95Index] ?? 0;
+    const p95Index = Math.floor(degreeRows.length * 0.95);
+    const p95Degree = degreeRows[p95Index]?.degree ?? 0;
     const godNodeCount = p95Degree > 0
-        ? [...degMap.values()].filter(d => d > p95Degree).length
+        ? degreeRows.filter(r => r.degree > p95Degree).length
         : 0;
     // ── Circular edges (bidirectional import pairs) ───────────────────────────
     const totalEdgesRow = db.prepare('SELECT COUNT(*) as c FROM edges').get();

package/dist/src/graph/health-score.js.map

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package/dist/src/graph/hotspots.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"hotspots.d.ts","sourceRoot":"","sources":["../../../src/graph/hotspots.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,QAAQ,MAAM,gBAAgB,CAAC;AAO3C,MAAM,WAAW,aAAa;IAC5B,MAAM,EAAE,MAAM,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,QAAQ,EAAE,MAAM,CAAC;IACjB,KAAK,EAAE,MAAM,CAAC;IACd,WAAW,EAAE,MAAM,GAAG,IAAI,CAAC;IAC3B,2EAA2E;IAC3E,UAAU,EAAE,MAAM,CAAC;IACnB,8CAA8C;IAC9C,cAAc,EAAE,MAAM,CAAC;IACvB,sCAAsC;IACtC,eAAe,EAAE,MAAM,CAAC;IACxB,2DAA2D;IAC3D,YAAY,EAAE,MAAM,CAAC;IACrB,oDAAoD;IACpD,KAAK,EAAE,cAAc,GAAG,QAAQ,GAAG,SAAS,CAAC;IAC7C,qCAAqC;IACrC,cAAc,EAAE,MAAM,GAAG,IAAI,CAAC;CAC/B;AAED;;;;;;;;;;GAUG;AACH,wBAAgB,eAAe,CAC7B,EAAE,EAAE,QAAQ,CAAC,QAAQ,EACrB,UAAU,EAAE,MAAM,EAClB,OAAO,GAAE;IACP,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,UAAU,CAAC,EAAE,MAAM,CAAC;CAChB,GACL,aAAa,EAAE,CAsIjB;AAED;;;;;GAKG;AACH,wBAAgB,cAAc,CAAC,QAAQ,EAAE,aAAa,EAAE,GAAG,MAAM,CA6BhE"}

package/dist/src/graph/hotspots.js

@@ -79,12 +79,16 @@ export function computeHotspots(db, projectDir, options = {}) {
     // ── Step 3: Get file nodes + centrality from DB ───────────────────────────
     const fileNodes = db.prepare(`
     SELECT n.id, n.name, n.file_path, n.label, n.community_id,
-           COUNT(DISTINCT e1.id) + COUNT(DISTINCT e2.id) as degree
+           COALESCE(d.deg, 0) as degree
     FROM nodes n
-    LEFT JOIN edges e1 ON e1.source_id = n.id
-    LEFT JOIN edges e2 ON e2.target_id = n.id
+    LEFT JOIN (
+      SELECT node_id, SUM(cnt) AS deg FROM (
+        SELECT source_id AS node_id, COUNT(*) AS cnt FROM edges GROUP BY source_id
+        UNION ALL
+        SELECT target_id AS node_id, COUNT(*) AS cnt FROM edges GROUP BY target_id
+      ) GROUP BY node_id
+    ) d ON d.node_id = n.id
     WHERE n.label = 'File' AND n.file_path IS NOT NULL
-    GROUP BY n.id
   `).all();
     // ── Step 4: Join churn + centrality ──────────────────────────────────────
     const results = [];

package/dist/src/graph/hotspots.js.map

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package/dist/src/graph/statistics.d.ts

@@ -24,8 +24,9 @@ export interface PathStats {
     diameter: number;
 }
 /**
- * Compute both average path length and graph diameter in a single BFS pass.
- * Unreachable pairs are excluded from averagePathLength.
+ * Compute both average path length and graph diameter via BFS.
+ * For graphs > 500 nodes, uses deterministic sampling (every Nth node)
+ * to keep runtime practical — O(sample * E) instead of O(N * E).
  */
 export declare function pathStats(db: MonographDb): PathStats;
 /**

package/dist/src/graph/statistics.d.ts.map

@@ -1 +1 @@
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