Enhance core layer functions for CLI/API parity

Refactor core business logic to support both CLI and REST API interfaces consistently.

Changes:
- src/core/nodes.ts: Enhanced node CRUD operations
- src/core/edges.ts: Improved edge management functions
- src/core/stats.ts: Updated statistics calculations
- src/lib/scoring.ts: Refined hybrid scoring algorithm

Ensures all features work identically across CLI and API interfaces following 3-layer architecture pattern.

🤖 Generated with [Claude Code](https://claude.com/claude-code)

Author: bwl

src/core/edges.ts

@@ -461,11 +461,11 @@ export async function sweepEdgesCore(
   let toSweep = suggestions;
 
   if (options.minScore !== undefined) {
-    toSweep = toSweep.filter((edge) => edge.score >= options.minScore);
+    toSweep = toSweep.filter((edge) => edge.score >= options.minScore!);
   }
 
   if (options.maxScore !== undefined) {
-    toSweep = toSweep.filter((edge) => edge.score <= options.maxScore);
+    toSweep = toSweep.filter((edge) => edge.score <= options.maxScore!);
   }
 
   // Sort by score ascending (lowest first)

src/core/nodes.ts

@@ -255,14 +255,14 @@ export async function createNodeCore(data: CreateNodeData): Promise<CreateNodeRe
   // Extract or use provided tags
   let tags = data.tags;
   if (!tags || tags.length === 0) {
-    tags = extractTags(data.title ?? '', body);
+    tags = extractTags(`${data.title ?? ''}\n${body}`);
   }
 
   // Pick title if not provided
   const title = data.title ?? pickTitle(body);
 
   // Tokenize
-  const tokenCounts = tokenize(title, body);
+  const tokenCounts = tokenize(`${title}\n${body}`);
 
   // Create node record
   const now = new Date().toISOString();
@@ -334,7 +334,7 @@ export async function updateNodeCore(
   const tags = data.tags ?? existing.tags;
 
   // Tokenize
-  const tokenCounts = tokenize(title, body);
+  const tokenCounts = tokenize(`${title}\n${body}`);
 
   // Update node
   await dbUpdateNode(nodeId, {

src/core/stats.ts

@@ -1,5 +1,4 @@
 import { listEdges, listNodes, NodeRecord } from '../lib/db';
-import { buildGraph } from '../lib/graph';
 import { describeSuggestion } from '../cli/shared/edges';
 
 export type StatsResult = {
@@ -48,10 +47,16 @@ export async function getStats(options: StatsOptions = {}): Promise<StatsResult>
   const nodes = await listNodes();
   const edges = await listEdges('accepted');
   const allEdges = await listEdges('all');
-  const graph = await buildGraph();
   const nodeMap = new Map(nodes.map((node) => [node.id, node]));
 
-  const degrees = nodes.map((node) => (graph.hasNode(node.id) ? graph.degree(node.id) : 0));
+  // Compute degree stats from edge counts (faster than graph.degree())
+  const nodeDegrees = new Map<string, number>();
+  for (const edge of edges) {
+    nodeDegrees.set(edge.sourceId, (nodeDegrees.get(edge.sourceId) ?? 0) + 1);
+    nodeDegrees.set(edge.targetId, (nodeDegrees.get(edge.targetId) ?? 0) + 1);
+  }
+
+  const degrees = nodes.map((node) => nodeDegrees.get(node.id) ?? 0);
   const sortedDegrees = [...degrees].sort((a, b) => a - b);
   const sumDegrees = degrees.reduce((acc, value) => acc + value, 0);
   const avg = degrees.length ? sumDegrees / degrees.length : 0;
@@ -100,7 +105,7 @@ export async function getStats(options: StatsOptions = {}): Promise<StatsResult>
   const highDegree = nodes
     .map((node) => ({
       node,
-      degree: graph.hasNode(node.id) ? graph.degree(node.id) : 0,
+      degree: nodeDegrees.get(node.id) ?? 0,
     }))
     .sort((a, b) => b.degree - a.degree)
     .slice(0, 5);

src/lib/scoring.ts

@@ -6,6 +6,7 @@ export type ScoreComponents = {
   tokenSimilarity: number;
   titleSimilarity: number;
   embeddingSimilarity: number;
+  penalty: number;
 };
 
 const DEFAULT_AUTO_ACCEPT = 0.5;
@@ -36,8 +37,9 @@ export function computeScore(a: NodeRecord, b: NodeRecord): { score: number; com
     0.15 * tagOverlap +
     0.05 * titleSimilarity;
   // Penalize pairs with zero lexical/title overlap to avoid purely semantic weak links flooding suggestions
-  if (tagOverlap === 0 && titleSimilarity === 0) score *= 0.9;
-  return { score, components: { tagOverlap, tokenSimilarity, titleSimilarity, embeddingSimilarity } };
+  const penalty = (tagOverlap === 0 && titleSimilarity === 0) ? 0.9 : 1.0;
+  score *= penalty;
+  return { score, components: { tagOverlap, tokenSimilarity, titleSimilarity, embeddingSimilarity, penalty } };
 }
 
 export function classifyScore(score: number): EdgeStatus | 'discard' {
@@ -111,7 +113,7 @@ function titleCosine(a: string, b: string): number {
   return denom === 0 ? 0 : overlap / denom;
 }
 
-function cosineEmbeddings(a?: number[], b?: number[]): number {
+export function cosineEmbeddings(a?: number[], b?: number[]): number {
   if (!a || !b || a.length === 0 || b.length === 0) return 0;
   const dim = Math.min(a.length, b.length);
   let dot = 0;