@monoes/monograph 1.1.0 → 1.2.1

package/dist/src/pipeline/cluster-only.js

@@ -0,0 +1,55 @@
+import { loadGraphFromDb } from '../graph/loader.js';
+import { leiden } from './phases/leiden.js';
+import louvain from 'graphology-communities-louvain';
+/**
+ * Re-run community detection without re-extracting the full pipeline.
+ * Reads edges from the DB, runs Leiden (Louvain-based) community detection,
+ * and writes community_id assignments back to the nodes table.
+ */
+export async function runClusterOnly(db) {
+    // Check if there are any edges at all
+    const edgeCount = db.prepare('SELECT COUNT(*) as cnt FROM edges').get().cnt;
+    if (edgeCount === 0) {
+        return { communityCount: 0, nodeCount: 0 };
+    }
+    // Build graphology graph from the DB
+    const graph = loadGraphFromDb(db);
+    if (graph.order === 0) {
+        return { communityCount: 0, nodeCount: 0 };
+    }
+    // Run community detection using Leiden (Louvain-based with refinement)
+    let communities = {};
+    try {
+        communities = leiden(graph, { seed: 42 });
+    }
+    catch (e) {
+        console.warn('[monograph] Leiden failed in cluster-only, falling back to Louvain:', e);
+        try {
+            communities = louvain(graph, { randomWalk: false });
+        }
+        catch {
+            // Assign all to community 0 as last resort
+            for (const nodeId of graph.nodes()) {
+                communities[nodeId] = 0;
+            }
+        }
+    }
+    // Write community assignments back to DB and count in a single pass
+    const updateStmt = db.prepare('UPDATE nodes SET community_id = ? WHERE id = ?');
+    const communityIds = new Set();
+    let nodeCount = 0;
+    const updateAll = db.transaction(() => {
+        for (const nodeId in communities) {
+            const commId = communities[nodeId];
+            updateStmt.run(commId, nodeId);
+            communityIds.add(commId);
+            nodeCount++;
+        }
+    });
+    updateAll();
+    return {
+        communityCount: communityIds.size,
+        nodeCount,
+    };
+}
+//# sourceMappingURL=cluster-only.js.map

package/dist/src/pipeline/cluster-only.js.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/effort.d.ts

@@ -0,0 +1,13 @@
+export type AnalysisEffort = 'low' | 'medium' | 'high';
+export interface EffortProfile {
+    runChurn: boolean;
+    runOwnership: boolean;
+    runHotspots: boolean;
+    runFileScores: boolean;
+    runSuffixArray: boolean;
+    runCrossReference: boolean;
+    maxFilesForExpensiveAnalysis: number;
+}
+export declare function getEffortProfile(effort?: AnalysisEffort): EffortProfile;
+export declare function parseEffort(s: string): AnalysisEffort;
+//# sourceMappingURL=effort.d.ts.map

package/dist/src/pipeline/effort.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/effort.js

@@ -0,0 +1,38 @@
+const EFFORT_PROFILES = {
+    low: {
+        runChurn: false,
+        runOwnership: false,
+        runHotspots: false,
+        runFileScores: true,
+        runSuffixArray: false,
+        runCrossReference: false,
+        maxFilesForExpensiveAnalysis: 100,
+    },
+    medium: {
+        runChurn: true,
+        runOwnership: false,
+        runHotspots: true,
+        runFileScores: true,
+        runSuffixArray: false,
+        runCrossReference: true,
+        maxFilesForExpensiveAnalysis: 500,
+    },
+    high: {
+        runChurn: true,
+        runOwnership: true,
+        runHotspots: true,
+        runFileScores: true,
+        runSuffixArray: true,
+        runCrossReference: true,
+        maxFilesForExpensiveAnalysis: Infinity,
+    },
+};
+export function getEffortProfile(effort = 'medium') {
+    return EFFORT_PROFILES[effort];
+}
+export function parseEffort(s) {
+    if (s === 'low' || s === 'medium' || s === 'high')
+        return s;
+    return 'medium';
+}
+//# sourceMappingURL=effort.js.map

package/dist/src/pipeline/effort.js.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/orchestrator.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"orchestrator.d.ts","sourceRoot":"","sources":["../../../src/pipeline/orchestrator.ts"],"names":[],"mappings":"AAwBA,OAAO,KAAK,EAAE,eAAe,EAAmB,MAAM,YAAY,CAAC;AAEnE,OAAO,KAAK,EAAE,gBAAgB,EAAqB,MAAM,aAAa,CAAC;AAWvE,MAAM,WAAW,YAAa,SAAQ,OAAO,CAAC,eAAe,CAAC;IAC5D,UAAU,CAAC,EAAE,CAAC,CAAC,EAAE,gBAAgB,KAAK,IAAI,CAAC;IAC3C,KAAK,CAAC,EAAE,OAAO,CAAC;IAChB,oGAAoG;IACpG,WAAW,CAAC,EAAE,OAAO,CAAC;CACvB;AAED,wBAAsB,UAAU,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,GAAE,YAAiB,GAAG,OAAO,CAAC,IAAI,CAAC,CAsD5F"}

package/dist/src/pipeline/orchestrator.js

@@ -1,20 +1,59 @@
 import { resolve, join } from 'path';
+import { execSync } from 'child_process';
 import Graph from 'graphology';
 import { openDb, closeDb } from '../storage/db.js';
 import { PipelineRunner } from './runner.js';
 import { scanPhase } from './phases/scan.js';
 import { structurePhase } from './phases/structure.js';
 import { parsePhase } from './phases/parse.js';
+import { markdownPhase } from './phases/markdown.js';
+import { routesPhase } from './phases/routes.js';
+import { toolsPhase } from './phases/tools.js';
+import { ormPhase } from './phases/orm.js';
 import { crossFilePhase } from './phases/cross-file.js';
+import { scopeResolutionPhase } from './phases/scope-resolution.js';
 import { mroPhase } from './phases/mro.js';
 import { communitiesPhase } from './phases/communities.js';
+import { processesPhase } from './phases/processes.js';
 import { godNodesPhase } from './phases/god-nodes.js';
 import { surprisesPhase } from './phases/surprises.js';
 import { suggestPhase } from './phases/suggest.js';
+import { variablesPhase } from './phases/variables-phase.js';
+import { wildcardSynthesisPhase } from './phases/wildcard-phase.js';
+import { frameworkDetectPhase } from './phases/framework-detect.js';
+import { importResolverPhase } from './phases/import-resolver.js';
 import { DEFAULT_OPTIONS } from './types.js';
+import { generateGraphReport } from '../reporting/graph-report.js';
+function getCurrentCommitHash(repoPath) {
+    try {
+        return execSync('git rev-parse HEAD', { cwd: repoPath, encoding: 'utf8' }).trim();
+    }
+    catch {
+        return null;
+    }
+}
 export async function buildAsync(repoPath, options = {}) {
     const dbPath = resolve(join(repoPath, '.monomind', 'monograph.db'));
     const fullOptions = { ...DEFAULT_OPTIONS, ...options };
+    // Incremental guard: if the caller requested skip-when-fresh and force is
+    // not set, check staleness before opening the DB for a full write cycle.
+    if (options.incremental && !options.force) {
+        const { existsSync: _existsSync } = await import('fs');
+        if (_existsSync(dbPath)) {
+            const { checkStaleness } = await import('../staleness/git-staleness.js');
+            const tmpDb = openDb(dbPath);
+            try {
+                const report = checkStaleness(tmpDb, resolve(repoPath));
+                if (!report.isStale && report.currentCommit !== null) {
+                    options.onProgress?.({ phase: 'skip', message: 'Index is fresh — skipping rebuild' });
+                    return; // Already up-to-date
+                }
+            }
+            finally {
+                closeDb(tmpDb);
+            }
+        }
+    }
     const db = openDb(dbPath);
     try {
         const graph = new Graph({ multi: true, type: 'directed' });
@@ -25,10 +64,19 @@ export async function buildAsync(repoPath, options = {}) {
             options: fullOptions,
         };
         const runner = new PipelineRunner([
-            scanPhase, structurePhase, parsePhase, crossFilePhase,
-            mroPhase, communitiesPhase, godNodesPhase, surprisesPhase, suggestPhase,
+            scanPhase, frameworkDetectPhase, structurePhase, parsePhase, variablesPhase,
+            markdownPhase, routesPhase, toolsPhase, ormPhase,
+            crossFilePhase, wildcardSynthesisPhase, importResolverPhase, scopeResolutionPhase,
+            mroPhase, communitiesPhase, processesPhase, godNodesPhase, surprisesPhase, suggestPhase,
         ]);
-        await runner.run(ctx);
+        const outputs = await runner.run(ctx);
+        const hash = getCurrentCommitHash(resolve(repoPath));
+        if (hash) {
+            db.prepare("INSERT OR REPLACE INTO index_meta VALUES ('last_commit_hash', ?)").run(hash);
+        }
+        const suggestOut = outputs.get('suggest');
+        const questions = suggestOut?.questions ?? [];
+        await generateGraphReport(resolve(repoPath), undefined, dbPath, questions);
     }
     finally {
         closeDb(db);

package/dist/src/pipeline/orchestrator.js.map

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package/dist/src/pipeline/phases/boundary.d.ts

@@ -0,0 +1,34 @@
+import type Database from 'better-sqlite3';
+export interface ZoneConfig {
+    name: string;
+    glob: string;
+}
+export interface MonographConfig {
+    zones?: ZoneConfig[];
+    allowedImports?: [string, string][];
+}
+export interface BoundaryViolation {
+    fromPath: string;
+    toPath: string;
+    fromZone: string;
+    toZone: string;
+    edgeRelation: string;
+}
+/**
+ * Load .monographrc.json from repoRoot. Returns empty config if not found or invalid.
+ */
+export declare function loadMonographConfig(repoRoot: string): MonographConfig;
+/**
+ * Classify a file path into a zone name. Returns null if no zone matches.
+ * Compiles the glob patterns on every call — use classifyZoneCompiled with
+ * precompiled zones for hot paths.
+ */
+export declare function classifyZone(filePath: string, zones: ZoneConfig[]): string | null;
+/**
+ * Check all edges in the DB for boundary violations.
+ * Violations are cross-zone edges not present in the allowedImports allowlist.
+ * Intra-zone imports are always allowed.
+ * Returns [] if no .monographrc.json or no zones defined.
+ */
+export declare function detectBoundaryViolations(db: Database.Database, repoRoot: string): BoundaryViolation[];
+//# sourceMappingURL=boundary.d.ts.map

package/dist/src/pipeline/phases/boundary.d.ts.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/phases/boundary.js

@@ -0,0 +1,113 @@
+import { existsSync, readFileSync } from 'fs';
+import { join } from 'path';
+/**
+ * Convert a glob pattern to a regex.
+ * Handles: ** to .*, * to [^/]*, escapes other regex chars.
+ */
+function globToRegex(glob) {
+    const DOUBLE_STAR = '\x00DS\x00';
+    const pattern = glob
+        .replace(/\*\*/g, DOUBLE_STAR)
+        .replace(/[.+^${}()|[\]\\]/g, '\\$&')
+        .replace(/\*/g, '[^/]*')
+        .split(DOUBLE_STAR).join('.*');
+    return new RegExp('^' + pattern + '$');
+}
+/** Compile a ZoneConfig[] into CompiledZone[] once to avoid reconstructing RegExps per path. */
+function compileZones(zones) {
+    return zones.map(z => ({ name: z.name, re: globToRegex(z.glob) }));
+}
+/**
+ * Classify a file path into a zone name using precompiled regexes.
+ * Returns null if no zone matches.
+ */
+function classifyZoneCompiled(filePath, compiled) {
+    for (const z of compiled) {
+        if (z.re.test(filePath))
+            return z.name;
+    }
+    return null;
+}
+/**
+ * Load .monographrc.json from repoRoot. Returns empty config if not found or invalid.
+ */
+export function loadMonographConfig(repoRoot) {
+    const configPath = join(repoRoot, '.monographrc.json');
+    if (!existsSync(configPath))
+        return {};
+    try {
+        const raw = readFileSync(configPath, 'utf-8');
+        return JSON.parse(raw);
+    }
+    catch {
+        return {};
+    }
+}
+/**
+ * Classify a file path into a zone name. Returns null if no zone matches.
+ * Compiles the glob patterns on every call — use classifyZoneCompiled with
+ * precompiled zones for hot paths.
+ */
+export function classifyZone(filePath, zones) {
+    for (const zone of zones) {
+        const regex = globToRegex(zone.glob);
+        if (regex.test(filePath))
+            return zone.name;
+    }
+    return null;
+}
+/**
+ * Check all edges in the DB for boundary violations.
+ * Violations are cross-zone edges not present in the allowedImports allowlist.
+ * Intra-zone imports are always allowed.
+ * Returns [] if no .monographrc.json or no zones defined.
+ */
+export function detectBoundaryViolations(db, repoRoot) {
+    const config = loadMonographConfig(repoRoot);
+    if (!config.zones || config.zones.length === 0)
+        return [];
+    const zones = config.zones;
+    const allowedSet = new Set((config.allowedImports ?? []).map(([from, to]) => `${from}→${to}`));
+    // Precompile zone regexes once — avoids re-constructing RegExp objects per file path.
+    const compiledZones = compileZones(zones);
+    const rows = db.prepare(`
+    SELECT e.id, e.relation,
+           ns.file_path AS src_path,
+           nt.file_path AS tgt_path
+    FROM edges e
+    JOIN nodes ns ON ns.id = e.source_id
+    JOIN nodes nt ON nt.id = e.target_id
+    WHERE ns.file_path IS NOT NULL AND nt.file_path IS NOT NULL
+  `).all();
+    // Cache per-path zone classification to avoid O(rows * zones) repeated regex tests.
+    const pathZoneCache = new Map();
+    const classifyPath = (p) => {
+        let zone = pathZoneCache.get(p);
+        if (zone === undefined) {
+            zone = classifyZoneCompiled(p, compiledZones);
+            pathZoneCache.set(p, zone);
+        }
+        return zone;
+    };
+    const violations = [];
+    for (const row of rows) {
+        const fromZone = classifyPath(row.src_path);
+        const toZone = classifyPath(row.tgt_path);
+        if (fromZone === null || toZone === null)
+            continue;
+        if (fromZone === toZone)
+            continue;
+        const key = `${fromZone}→${toZone}`;
+        if (!allowedSet.has(key)) {
+            violations.push({
+                fromPath: row.src_path,
+                toPath: row.tgt_path,
+                fromZone,
+                toZone,
+                edgeRelation: row.relation,
+            });
+        }
+    }
+    return violations;
+}
+//# sourceMappingURL=boundary.js.map

package/dist/src/pipeline/phases/boundary.js.map

@@ -0,0 +1 @@
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package/dist/src/pipeline/phases/communities.d.ts

@@ -2,6 +2,30 @@ import type { PipelinePhase } from '../types.js';
 export interface CommunitiesOutput {
     memberships: Map<string, number>;
     communityLabels: Map<number, string>;
+    cohesionScores: Map<number, number>;
 }
+export declare function computeCohesion(communityId: number, memberships: Map<string, number>, edges: Array<{
+    sourceId: string;
+    targetId: string;
+}>): number;
+/**
+ * Compute cohesion scores for all communities in a single O(N+E) pass.
+ *
+ * This replaces calling `computeCohesion` inside a loop, which was O(K*(N+E))
+ * because each call re-scanned all memberships (O(N)) and all edges (O(E)).
+ *
+ * @param memberships - nodeId → communityId map from the clustering step
+ * @param edges - all edges used for the graph (IMPORTS + resolved)
+ * @returns Map of communityId → cohesion score ∈ [0, 1]
+ */
+export declare function computeAllCohesionScores(memberships: Map<string, number>, edges: Array<{
+    sourceId: string;
+    targetId: string;
+}>): Map<number, number>;
 export declare const communitiesPhase: PipelinePhase<CommunitiesOutput>;
+/**
+ * Split a community that is too large into smaller sub-groups.
+ * By graphify convention, communities >25% of total graph nodes are split.
+ */
+export declare function splitOversizedCommunity(memberIds: string[], maxGroupSize: number): string[][];
 //# sourceMappingURL=communities.d.ts.map

package/dist/src/pipeline/phases/communities.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"communities.d.ts","sourceRoot":"","sources":["../../../../src/pipeline/phases/communities.ts"],"names":[],"mappings":"AAEA,OAAO,KAAK,EAAE,aAAa,EAAmB,MAAM,aAAa,CAAC;AAMlE,MAAM,WAAW,iBAAiB;IAChC,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,eAAe,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACrC,cAAc,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACrC;AAED,wBAAgB,eAAe,CAC7B,WAAW,EAAE,MAAM,EACnB,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAChC,KAAK,EAAE,KAAK,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,GACnD,MAAM,CAsBR;AAED;;;;;;;;;GASG;AACH,wBAAgB,wBAAwB,CACtC,WAAW,EAAE,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,EAChC,KAAK,EAAE,KAAK,CAAC;IAAE,QAAQ,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,CAAC,GACnD,GAAG,CAAC,MAAM,EAAE,MAAM,CAAC,CAiDrB;AAED,eAAO,MAAM,gBAAgB,EAAE,aAAa,CAAC,iBAAiB,CAwC7D,CAAC;AAEF;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,SAAS,EAAE,MAAM,EAAE,EAAE,YAAY,EAAE,MAAM,GAAG,MAAM,EAAE,EAAE,CAO7F"}

package/dist/src/pipeline/phases/communities.js

@@ -1,8 +1,88 @@
 import louvain from 'graphology-communities-louvain';
+import { leiden } from './leiden.js';
 import { loadGraphFromEdges } from '../../graph/loader.js';
+export function computeCohesion(communityId, memberships, edges) {
+    const members = [...memberships.entries()].filter(([, c]) => c === communityId).map(([id]) => id);
+    const n = members.length;
+    if (n <= 1)
+        return 1;
+    const memberSet = new Set(members);
+    const maxEdges = (n * (n - 1)) / 2; // undirected: n*(n-1)/2
+    if (maxEdges === 0)
+        return 1;
+    // Count unique undirected internal edges
+    const seen = new Set();
+    let internalCount = 0;
+    for (const e of edges) {
+        if (memberSet.has(e.sourceId) && memberSet.has(e.targetId)) {
+            const key = [e.sourceId, e.targetId].sort().join('\0');
+            if (!seen.has(key)) {
+                seen.add(key);
+                internalCount++;
+            }
+        }
+    }
+    return internalCount / maxEdges;
+}
+/**
+ * Compute cohesion scores for all communities in a single O(N+E) pass.
+ *
+ * This replaces calling `computeCohesion` inside a loop, which was O(K*(N+E))
+ * because each call re-scanned all memberships (O(N)) and all edges (O(E)).
+ *
+ * @param memberships - nodeId → communityId map from the clustering step
+ * @param edges - all edges used for the graph (IMPORTS + resolved)
+ * @returns Map of communityId → cohesion score ∈ [0, 1]
+ */
+export function computeAllCohesionScores(memberships, edges) {
+    // Single pass over memberships: build communityId → Set<nodeId>
+    const memberSets = new Map();
+    for (const [nodeId, commId] of memberships) {
+        let s = memberSets.get(commId);
+        if (!s) {
+            s = new Set();
+            memberSets.set(commId, s);
+        }
+        s.add(nodeId);
+    }
+    // Single pass over edges: count unique undirected internal edges per community
+    const internalEdgeCounts = new Map();
+    const seenEdgeKeys = new Map();
+    for (const e of edges) {
+        const commSrc = memberships.get(e.sourceId);
+        const commTgt = memberships.get(e.targetId);
+        if (commSrc === undefined || commTgt === undefined || commSrc !== commTgt)
+            continue;
+        let seen = seenEdgeKeys.get(commSrc);
+        if (!seen) {
+            seen = new Set();
+            seenEdgeKeys.set(commSrc, seen);
+        }
+        const key = e.sourceId < e.targetId
+            ? `${e.sourceId}\0${e.targetId}`
+            : `${e.targetId}\0${e.sourceId}`;
+        if (!seen.has(key)) {
+            seen.add(key);
+            internalEdgeCounts.set(commSrc, (internalEdgeCounts.get(commSrc) ?? 0) + 1);
+        }
+    }
+    // Compute final scores
+    const scores = new Map();
+    for (const [commId, members] of memberSets) {
+        const n = members.size;
+        if (n <= 1) {
+            scores.set(commId, 1);
+            continue;
+        }
+        const maxEdges = (n * (n - 1)) / 2;
+        const internalCount = internalEdgeCounts.get(commId) ?? 0;
+        scores.set(commId, maxEdges > 0 ? internalCount / maxEdges : 1);
+    }
+    return scores;
+}
 export const communitiesPhase = {
     name: 'communities',
-    deps: ['cross-file', 'mro'],
+    deps: ['parse', 'cross-file', 'mro'],
     async execute(_ctx, deps) {
         const { resolvedEdges } = deps.get('cross-file');
         const { allEdges } = deps.get('parse');
@@ -10,10 +90,16 @@ export const communitiesPhase = {
         const graph = loadGraphFromEdges(allUsedEdges);
         let communities = {};
         try {
-            communities = louvain(graph);
+            communities = leiden(graph, { seed: 42 });
         }
-        catch {
-            // Empty or disconnected graph
+        catch (e) {
+            console.warn('[monograph] Leiden failed, falling back to Louvain:', e);
+            try {
+                communities = louvain(graph, { randomWalk: false });
+            }
+            catch {
+                // Empty or disconnected graph
+            }
         }
         const memberships = new Map(Object.entries(communities).map(([k, v]) => [k, v]));
         const communityLabels = new Map();
@@ -28,7 +114,22 @@ export const communitiesPhase = {
             const topNode = [...nodeDegs.entries()].sort((a, b) => b[1] - a[1])[0]?.[0] ?? '';
             communityLabels.set(commId, `community-${commId}(${topNode.slice(0, 20)})`);
         }
-        return { memberships, communityLabels };
+        // Compute all cohesion scores in one O(N+E) pass instead of O(K*(N+E))
+        const cohesionScores = computeAllCohesionScores(memberships, allUsedEdges);
+        return { memberships, communityLabels, cohesionScores };
     },
 };
+/**
+ * Split a community that is too large into smaller sub-groups.
+ * By graphify convention, communities >25% of total graph nodes are split.
+ */
+export function splitOversizedCommunity(memberIds, maxGroupSize) {
+    if (memberIds.length <= maxGroupSize)
+        return [memberIds];
+    const groups = [];
+    for (let i = 0; i < memberIds.length; i += maxGroupSize) {
+        groups.push(memberIds.slice(i, i + maxGroupSize));
+    }
+    return groups;
+}
 //# sourceMappingURL=communities.js.map

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package/dist/src/pipeline/phases/contextual-proximity.d.ts

@@ -0,0 +1,7 @@
+import type { PipelinePhase } from '../types.js';
+export interface ContextualProximityOutput {
+    coOccursEdges: number;
+    conceptsScored: number;
+}
+export declare const contextualProximityPhase: PipelinePhase<ContextualProximityOutput>;
+//# sourceMappingURL=contextual-proximity.d.ts.map

package/dist/src/pipeline/phases/contextual-proximity.d.ts.map

@@ -0,0 +1 @@
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