@optave/codegraph 3.1.4 → 3.1.5

package/src/{branch-compare.js → features/branch-compare.js}

@@ -11,9 +11,9 @@ import fs from 'node:fs';
 import os from 'node:os';
 import path from 'node:path';
 import Database from 'better-sqlite3';
-import { buildGraph } from './builder.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { kindIcon } from './queries.js';
+import { buildGraph } from '../domain/graph/builder.js';
+import { kindIcon } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 
 // ─── Git Helpers ────────────────────────────────────────────────────────
 

package/src/{cfg.js → features/cfg.js}

@@ -7,14 +7,14 @@
 
 import fs from 'node:fs';
 import path from 'node:path';
-import { CFG_RULES } from './ast-analysis/rules/index.js';
+import { CFG_RULES } from '../ast-analysis/rules/index.js';
 import {
   makeCfgRules as _makeCfgRules,
   buildExtensionSet,
   buildExtToLangMap,
-} from './ast-analysis/shared.js';
-import { walkWithVisitors } from './ast-analysis/visitor.js';
-import { createCfgVisitor } from './ast-analysis/visitors/cfg-visitor.js';
+} from '../ast-analysis/shared.js';
+import { walkWithVisitors } from '../ast-analysis/visitor.js';
+import { createCfgVisitor } from '../ast-analysis/visitors/cfg-visitor.js';
 import {
   deleteCfgForNode,
   getCfgBlocks,
@@ -22,10 +22,10 @@ import {
   getFunctionNodeId,
   hasCfgTables,
   openReadonlyOrFail,
-} from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { info } from './logger.js';
-import { paginateResult } from './paginate.js';
+} from '../db/index.js';
+import { info } from '../infrastructure/logger.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../shared/paginate.js';
 
 // Re-export for backward compatibility
 export { _makeCfgRules as makeCfgRules, CFG_RULES };
@@ -104,13 +104,13 @@ export async function buildCFGData(db, fileSymbols, rootDir, _engineOpts) {
   }
 
   if (needsFallback) {
-    const { createParsers } = await import('./parser.js');
+    const { createParsers } = await import('../domain/parser.js');
     parsers = await createParsers();
   }
 
   let getParserFn = null;
   if (parsers) {
-    const mod = await import('./parser.js');
+    const mod = await import('../domain/parser.js');
     getParserFn = mod.getParser;
   }
 

package/src/{check.js → features/check.js}

@@ -1,10 +1,11 @@
 import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
-import { loadConfig } from './config.js';
-import { findCycles } from './cycles.js';
-import { findDbPath, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
+import { findDbPath, openReadonlyOrFail } from '../db/index.js';
+import { bfsTransitiveCallers } from '../domain/analysis/impact.js';
+import { findCycles } from '../domain/graph/cycles.js';
+import { loadConfig } from '../infrastructure/config.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 import { matchOwners, parseCodeowners } from './owners.js';
 
 // ─── Diff Parser ──────────────────────────────────────────────────────
@@ -96,31 +97,10 @@ export function checkMaxBlastRadius(db, changedRanges, threshold, noTests, maxDe
       }
       if (!overlaps) continue;
 
-      // BFS transitive callers
-      const visited = new Set([def.id]);
-      let frontier = [def.id];
-      let totalCallers = 0;
-      for (let d = 1; d <= maxDepth; d++) {
-        const nextFrontier = [];
-        for (const fid of frontier) {
-          const callers = db
-            .prepare(
-              `SELECT DISTINCT n.id, n.name, n.kind, n.file, n.line
-               FROM edges e JOIN nodes n ON e.source_id = n.id
-               WHERE e.target_id = ? AND e.kind = 'calls'`,
-            )
-            .all(fid);
-          for (const c of callers) {
-            if (!visited.has(c.id) && (!noTests || !isTestFile(c.file))) {
-              visited.add(c.id);
-              nextFrontier.push(c.id);
-              totalCallers++;
-            }
-          }
-        }
-        frontier = nextFrontier;
-        if (frontier.length === 0) break;
-      }
+      const { totalDependents: totalCallers } = bfsTransitiveCallers(db, def.id, {
+        noTests,
+        maxDepth,
+      });
 
       if (totalCallers > maxFound) maxFound = totalCallers;
       if (totalCallers > threshold) {
@@ -240,7 +220,10 @@ export function checkData(customDbPath, opts = {}) {
     const maxDepth = opts.depth || 3;
 
     // Load config defaults for check predicates
-    const config = loadConfig(repoRoot);
+    // NOTE: opts.config is loaded from process.cwd() at startup (via CLI context),
+    // which may differ from the DB's parent repo root when --db points to an external
+    // project. This is an acceptable trade-off to avoid duplicate I/O on the hot path.
+    const config = opts.config || loadConfig(repoRoot);
     const checkConfig = config.check || {};
 
     // Resolve which predicates are enabled: CLI flags ?? config ?? built-in defaults

package/src/{cochange.js → features/cochange.js}

@@ -8,11 +8,11 @@
 import { execFileSync } from 'node:child_process';
 import fs from 'node:fs';
 import path from 'node:path';
-import { normalizePath } from './constants.js';
-import { closeDb, findDbPath, initSchema, openDb, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { warn } from './logger.js';
-import { paginateResult } from './paginate.js';
+import { closeDb, findDbPath, initSchema, openDb, openReadonlyOrFail } from '../db/index.js';
+import { warn } from '../infrastructure/logger.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { normalizePath } from '../shared/constants.js';
+import { paginateResult } from '../shared/paginate.js';
 
 /**
  * Scan git history and return parsed commit data.

package/src/{communities.js → features/communities.js}

@@ -1,8 +1,8 @@
 import path from 'node:path';
-import { openReadonlyOrFail } from './db.js';
-import { louvainCommunities } from './graph/algorithms/louvain.js';
-import { buildDependencyGraph } from './graph/builders/dependency.js';
-import { paginateResult } from './paginate.js';
+import { openRepo } from '../db/index.js';
+import { louvainCommunities } from '../graph/algorithms/louvain.js';
+import { buildDependencyGraph } from '../graph/builders/dependency.js';
+import { paginateResult } from '../shared/paginate.js';
 
 // ─── Directory Helpers ────────────────────────────────────────────────
 
@@ -26,15 +26,15 @@ function getDirectory(filePath) {
  * @returns {{ communities: object[], modularity: number, drift: object, summary: object }}
  */
 export function communitiesData(customDbPath, opts = {}) {
-  const db = openReadonlyOrFail(customDbPath);
+  const { repo, close } = openRepo(customDbPath, opts);
   let graph;
   try {
-    graph = buildDependencyGraph(db, {
+    graph = buildDependencyGraph(repo, {
       fileLevel: !opts.functions,
       noTests: opts.noTests,
     });
   } finally {
-    db.close();
+    close();
   }
 
   // Handle empty or trivial graphs

package/src/{complexity.js → features/complexity.js}

@@ -3,20 +3,20 @@ import path from 'node:path';
 import {
   computeLOCMetrics as _computeLOCMetrics,
   computeMaintainabilityIndex as _computeMaintainabilityIndex,
-} from './ast-analysis/metrics.js';
-import { COMPLEXITY_RULES, HALSTEAD_RULES } from './ast-analysis/rules/index.js';
+} from '../ast-analysis/metrics.js';
+import { COMPLEXITY_RULES, HALSTEAD_RULES } from '../ast-analysis/rules/index.js';
 import {
   findFunctionNode as _findFunctionNode,
   buildExtensionSet,
   buildExtToLangMap,
-} from './ast-analysis/shared.js';
-import { walkWithVisitors } from './ast-analysis/visitor.js';
-import { createComplexityVisitor } from './ast-analysis/visitors/complexity-visitor.js';
-import { loadConfig } from './config.js';
-import { getFunctionNodeId, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { info } from './logger.js';
-import { paginateResult } from './paginate.js';
+} from '../ast-analysis/shared.js';
+import { walkWithVisitors } from '../ast-analysis/visitor.js';
+import { createComplexityVisitor } from '../ast-analysis/visitors/complexity-visitor.js';
+import { getFunctionNodeId, openReadonlyOrFail } from '../db/index.js';
+import { loadConfig } from '../infrastructure/config.js';
+import { info } from '../infrastructure/logger.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../shared/paginate.js';
 
 // Re-export rules for backward compatibility
 export { COMPLEXITY_RULES, HALSTEAD_RULES };
@@ -360,12 +360,12 @@ export async function buildComplexityMetrics(db, fileSymbols, rootDir, _engineOp
     }
   }
   if (needsFallback) {
-    const { createParsers } = await import('./parser.js');
+    const { createParsers } = await import('../domain/parser.js');
     parsers = await createParsers();
     extToLang = buildExtToLangMap();
   }
 
-  const { getParser } = await import('./parser.js');
+  const { getParser } = await import('../domain/parser.js');
 
   const upsert = db.prepare(
     `INSERT OR REPLACE INTO function_complexity
@@ -524,7 +524,7 @@ export function complexityData(customDbPath, opts = {}) {
     const kindFilter = opts.kind || null;
 
     // Load thresholds from config
-    const config = loadConfig(process.cwd());
+    const config = opts.config || loadConfig(process.cwd());
     const thresholds = config.manifesto?.rules || {
       cognitive: { warn: 15, fail: null },
       cyclomatic: { warn: 10, fail: null },

package/src/{dataflow.js → features/dataflow.js}

@@ -11,19 +11,19 @@
 
 import fs from 'node:fs';
 import path from 'node:path';
-import { DATAFLOW_RULES } from './ast-analysis/rules/index.js';
+import { DATAFLOW_RULES } from '../ast-analysis/rules/index.js';
 import {
   makeDataflowRules as _makeDataflowRules,
   buildExtensionSet,
   buildExtToLangMap,
-} from './ast-analysis/shared.js';
-import { walkWithVisitors } from './ast-analysis/visitor.js';
-import { createDataflowVisitor } from './ast-analysis/visitors/dataflow-visitor.js';
-import { hasDataflowTable, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { info } from './logger.js';
-import { paginateResult } from './paginate.js';
-import { ALL_SYMBOL_KINDS, normalizeSymbol } from './queries.js';
+} from '../ast-analysis/shared.js';
+import { walkWithVisitors } from '../ast-analysis/visitor.js';
+import { createDataflowVisitor } from '../ast-analysis/visitors/dataflow-visitor.js';
+import { hasDataflowTable, openReadonlyOrFail } from '../db/index.js';
+import { ALL_SYMBOL_KINDS, normalizeSymbol } from '../domain/queries.js';
+import { info } from '../infrastructure/logger.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../shared/paginate.js';
 
 // Re-export for backward compatibility
 export { _makeDataflowRules as makeDataflowRules, DATAFLOW_RULES };
@@ -88,13 +88,13 @@ export async function buildDataflowEdges(db, fileSymbols, rootDir, _engineOpts)
   }
 
   if (needsFallback) {
-    const { createParsers } = await import('./parser.js');
+    const { createParsers } = await import('../domain/parser.js');
     parsers = await createParsers();
   }
 
   let getParserFn = null;
   if (parsers) {
-    const mod = await import('./parser.js');
+    const mod = await import('../domain/parser.js');
     getParserFn = mod.getParser;
   }
 

package/src/{export.js → features/export.js}

@@ -1,6 +1,5 @@
 import path from 'node:path';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { paginateResult } from './paginate.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 import {
   renderFileLevelDOT,
   renderFileLevelGraphML,
@@ -10,7 +9,8 @@ import {
   renderFunctionLevelGraphML,
   renderFunctionLevelMermaid,
   renderFunctionLevelNeo4jCSV,
-} from './presentation/export.js';
+} from '../presentation/export.js';
+import { paginateResult } from '../shared/paginate.js';
 
 const DEFAULT_MIN_CONFIDENCE = 0.5;
 

package/src/{flow.js → features/flow.js}

@@ -5,10 +5,10 @@
  * framework entry points (routes, commands, events) through their call chains.
  */
 
-import { openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { paginateResult } from './paginate.js';
-import { CORE_SYMBOL_KINDS, findMatchingNodes } from './queries.js';
+import { openReadonlyOrFail } from '../db/index.js';
+import { CORE_SYMBOL_KINDS, findMatchingNodes } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../shared/paginate.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
 /**

package/src/{viewer.js → features/graph-enrichment.js}

@@ -1,16 +1,16 @@
 import path from 'node:path';
-import { louvainCommunities } from './graph/algorithms/louvain.js';
-import { CodeGraph } from './graph/model.js';
-import { isTestFile } from './infrastructure/test-filter.js';
+import { louvainCommunities } from '../graph/algorithms/louvain.js';
+import { CodeGraph } from '../graph/model.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 import {
   COMMUNITY_COLORS,
   DEFAULT_NODE_COLORS,
   DEFAULT_ROLE_COLORS,
-} from './presentation/colors.js';
-import { DEFAULT_CONFIG, renderPlotHTML } from './presentation/viewer.js';
+} from '../presentation/colors.js';
+import { DEFAULT_CONFIG, renderPlotHTML } from '../presentation/viewer.js';
 
 // Re-export presentation utilities for backward compatibility
-export { loadPlotConfig } from './presentation/viewer.js';
+export { loadPlotConfig } from '../presentation/viewer.js';
 
 const DEFAULT_MIN_CONFIDENCE = 0.5;
 

package/src/{manifesto.js → features/manifesto.js}

@@ -1,9 +1,9 @@
+import { openReadonlyOrFail } from '../db/index.js';
+import { findCycles } from '../domain/graph/cycles.js';
+import { loadConfig } from '../infrastructure/config.js';
+import { debug } from '../infrastructure/logger.js';
+import { paginateResult } from '../shared/paginate.js';
 import { evaluateBoundaries } from './boundaries.js';
-import { loadConfig } from './config.js';
-import { findCycles } from './cycles.js';
-import { openReadonlyOrFail } from './db.js';
-import { debug } from './logger.js';
-import { paginateResult } from './paginate.js';
 
 // ─── Rule Definitions ─────────────────────────────────────────────────
 
@@ -395,7 +395,7 @@ export function manifestoData(customDbPath, opts = {}) {
   const db = openReadonlyOrFail(customDbPath);
 
   try {
-    const config = loadConfig(process.cwd());
+    const config = opts.config || loadConfig(process.cwd());
     const rules = resolveRules(config.manifesto?.rules);
 
     const violations = [];

package/src/{owners.js → features/owners.js}

@@ -1,7 +1,7 @@
 import fs from 'node:fs';
 import path from 'node:path';
-import { findDbPath, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
+import { findDbPath, openReadonlyOrFail } from '../db/index.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
 
 // ─── CODEOWNERS Parsing ──────────────────────────────────────────────
 

package/src/{sequence.js → features/sequence.js}

@@ -6,10 +6,11 @@
  * sequence-diagram conventions.
  */
 
-import { findCallees, openReadonlyOrFail } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { paginateResult } from './paginate.js';
-import { findMatchingNodes } from './queries.js';
+import { openRepo } from '../db/index.js';
+import { SqliteRepository } from '../db/repository/sqlite-repository.js';
+import { findMatchingNodes } from '../domain/queries.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../shared/paginate.js';
 import { FRAMEWORK_ENTRY_PREFIXES } from './structure.js';
 
 // ─── Alias generation ────────────────────────────────────────────────
@@ -85,19 +86,19 @@ function buildAliases(files) {
  * @returns {{ entry, participants, messages, depth, totalMessages, truncated }}
  */
 export function sequenceData(name, dbPath, opts = {}) {
-  const db = openReadonlyOrFail(dbPath);
+  const { repo, close } = openRepo(dbPath, opts);
   try {
     const maxDepth = opts.depth || 10;
     const noTests = opts.noTests || false;
     const withDataflow = opts.dataflow || false;
 
     // Phase 1: Direct LIKE match
-    let matchNode = findMatchingNodes(db, name, opts)[0] ?? null;
+    let matchNode = findMatchingNodes(repo, name, opts)[0] ?? null;
 
     // Phase 2: Prefix-stripped matching
     if (!matchNode) {
       for (const prefix of FRAMEWORK_ENTRY_PREFIXES) {
-        matchNode = findMatchingNodes(db, `${prefix}${name}`, opts)[0] ?? null;
+        matchNode = findMatchingNodes(repo, `${prefix}${name}`, opts)[0] ?? null;
         if (matchNode) break;
       }
     }
@@ -133,7 +134,7 @@ export function sequenceData(name, dbPath, opts = {}) {
       const nextFrontier = [];
 
       for (const fid of frontier) {
-        const callees = findCallees(db, fid);
+        const callees = repo.findCallees(fid);
 
         const caller = idToNode.get(fid);
 
@@ -163,18 +164,17 @@ export function sequenceData(name, dbPath, opts = {}) {
 
       if (d === maxDepth && frontier.length > 0) {
         // Only mark truncated if at least one frontier node has further callees
-        const hasMoreCalls = frontier.some((fid) => findCallees(db, fid).length > 0);
+        const hasMoreCalls = frontier.some((fid) => repo.findCallees(fid).length > 0);
         if (hasMoreCalls) truncated = true;
       }
     }
 
     // Dataflow annotations: add return arrows
     if (withDataflow && messages.length > 0) {
-      const hasTable = db
-        .prepare("SELECT name FROM sqlite_master WHERE type='table' AND name='dataflow'")
-        .get();
+      const hasTable = repo.hasDataflowTable();
 
-      if (hasTable) {
+      if (hasTable && repo instanceof SqliteRepository) {
+        const db = repo.db;
         // Build name|file lookup for O(1) target node access
         const nodeByNameFile = new Map();
         for (const n of idToNode.values()) {
@@ -281,9 +281,9 @@ export function sequenceData(name, dbPath, opts = {}) {
     }
     return result;
   } finally {
-    db.close();
+    close();
   }
 }
 
 // Re-export Mermaid renderer from presentation layer
-export { sequenceToMermaid } from './presentation/sequence-renderer.js';
+export { sequenceToMermaid } from '../presentation/sequence-renderer.js';

package/src/{snapshot.js → features/snapshot.js}

@@ -1,9 +1,9 @@
 import fs from 'node:fs';
 import path from 'node:path';
 import Database from 'better-sqlite3';
-import { findDbPath } from './db.js';
-import { ConfigError, DbError } from './errors.js';
-import { debug } from './logger.js';
+import { findDbPath } from '../db/index.js';
+import { debug } from '../infrastructure/logger.js';
+import { ConfigError, DbError } from '../shared/errors.js';
 
 const NAME_RE = /^[a-zA-Z0-9_-]+$/;
 

package/src/{structure.js → features/structure.js}

@@ -1,9 +1,9 @@
 import path from 'node:path';
-import { normalizePath } from './constants.js';
-import { getNodeId, openReadonlyOrFail, testFilterSQL } from './db.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { debug } from './logger.js';
-import { paginateResult } from './paginate.js';
+import { getNodeId, openReadonlyOrFail, testFilterSQL } from '../db/index.js';
+import { debug } from '../infrastructure/logger.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { normalizePath } from '../shared/constants.js';
+import { paginateResult } from '../shared/paginate.js';
 
 // ─── Build-time: insert directory nodes, contains edges, and metrics ────
 
@@ -313,9 +313,9 @@ export function buildStructure(db, fileSymbols, _rootDir, lineCountMap, director
 // ─── Node role classification ─────────────────────────────────────────
 
 // Re-export from classifier for backward compatibility
-export { FRAMEWORK_ENTRY_PREFIXES } from './graph/classifiers/roles.js';
+export { FRAMEWORK_ENTRY_PREFIXES } from '../graph/classifiers/roles.js';
 
-import { classifyRoles } from './graph/classifiers/roles.js';
+import { classifyRoles } from '../graph/classifiers/roles.js';
 
 export function classifyNodeRoles(db) {
   const rows = db

package/src/{triage.js → features/triage.js}

@@ -1,8 +1,8 @@
-import { findNodesForTriage, openReadonlyOrFail } from './db.js';
-import { DEFAULT_WEIGHTS, scoreRisk } from './graph/classifiers/risk.js';
-import { isTestFile } from './infrastructure/test-filter.js';
-import { warn } from './logger.js';
-import { paginateResult } from './paginate.js';
+import { openRepo } from '../db/index.js';
+import { DEFAULT_WEIGHTS, scoreRisk } from '../graph/classifiers/risk.js';
+import { warn } from '../infrastructure/logger.js';
+import { isTestFile } from '../infrastructure/test-filter.js';
+import { paginateResult } from '../shared/paginate.js';
 
 // ─── Data Function ────────────────────────────────────────────────────
 
@@ -14,7 +14,7 @@ import { paginateResult } from './paginate.js';
  * @returns {{ items: object[], summary: object, _pagination?: object }}
  */
 export function triageData(customDbPath, opts = {}) {
-  const db = openReadonlyOrFail(customDbPath);
+  const { repo, close } = openRepo(customDbPath, opts);
   try {
     const noTests = opts.noTests || false;
     const fileFilter = opts.file || null;
@@ -26,7 +26,7 @@ export function triageData(customDbPath, opts = {}) {
 
     let rows;
     try {
-      rows = findNodesForTriage(db, {
+      rows = repo.findNodesForTriage({
         noTests,
         file: fileFilter,
         kind: kindFilter,
@@ -115,7 +115,7 @@ export function triageData(customDbPath, opts = {}) {
       offset: opts.offset,
     });
   } finally {
-    db.close();
+    close();
   }
 }
 

package/src/graph/builders/dependency.js

@@ -3,32 +3,39 @@
  * Replaces inline graph construction in cycles.js, communities.js, viewer.js, export.js.
  */
 
-import { getCallableNodes, getCallEdges, getFileNodesAll, getImportEdges } from '../../db.js';
+import {
+  getCallableNodes,
+  getCallEdges,
+  getFileNodesAll,
+  getImportEdges,
+  Repository,
+} from '../../db/index.js';
 import { isTestFile } from '../../infrastructure/test-filter.js';
 import { CodeGraph } from '../model.js';
 
 /**
- * @param {object} db - Open better-sqlite3 database (readonly)
+ * @param {object} dbOrRepo - Open better-sqlite3 database (readonly) or a Repository instance
  * @param {object} [opts]
  * @param {boolean} [opts.fileLevel=true] - File-level (imports) or function-level (calls)
  * @param {boolean} [opts.noTests=false] - Exclude test files
  * @param {number}  [opts.minConfidence] - Minimum edge confidence (function-level only)
  * @returns {CodeGraph}
  */
-export function buildDependencyGraph(db, opts = {}) {
+export function buildDependencyGraph(dbOrRepo, opts = {}) {
   const fileLevel = opts.fileLevel !== false;
   const noTests = opts.noTests || false;
 
   if (fileLevel) {
-    return buildFileLevelGraph(db, noTests);
+    return buildFileLevelGraph(dbOrRepo, noTests);
   }
-  return buildFunctionLevelGraph(db, noTests, opts.minConfidence);
+  return buildFunctionLevelGraph(dbOrRepo, noTests, opts.minConfidence);
 }
 
-function buildFileLevelGraph(db, noTests) {
+function buildFileLevelGraph(dbOrRepo, noTests) {
   const graph = new CodeGraph();
+  const isRepo = dbOrRepo instanceof Repository;
 
-  let nodes = getFileNodesAll(db);
+  let nodes = isRepo ? dbOrRepo.getFileNodesAll() : getFileNodesAll(dbOrRepo);
   if (noTests) nodes = nodes.filter((n) => !isTestFile(n.file));
 
   const nodeIds = new Set();
@@ -37,7 +44,7 @@ function buildFileLevelGraph(db, noTests) {
     nodeIds.add(n.id);
   }
 
-  const edges = getImportEdges(db);
+  const edges = isRepo ? dbOrRepo.getImportEdges() : getImportEdges(dbOrRepo);
   for (const e of edges) {
     if (!nodeIds.has(e.source_id) || !nodeIds.has(e.target_id)) continue;
     const src = String(e.source_id);
@@ -51,10 +58,11 @@ function buildFileLevelGraph(db, noTests) {
   return graph;
 }
 
-function buildFunctionLevelGraph(db, noTests, minConfidence) {
+function buildFunctionLevelGraph(dbOrRepo, noTests, minConfidence) {
   const graph = new CodeGraph();
+  const isRepo = dbOrRepo instanceof Repository;
 
-  let nodes = getCallableNodes(db);
+  let nodes = isRepo ? dbOrRepo.getCallableNodes() : getCallableNodes(dbOrRepo);
   if (noTests) nodes = nodes.filter((n) => !isTestFile(n.file));
 
   const nodeIds = new Set();
@@ -70,11 +78,22 @@ function buildFunctionLevelGraph(db, noTests, minConfidence) {
 
   let edges;
   if (minConfidence != null) {
-    edges = db
-      .prepare("SELECT source_id, target_id FROM edges WHERE kind = 'calls' AND confidence >= ?")
-      .all(minConfidence);
+    if (isRepo) {
+      // Trade-off: Repository.getCallEdges() returns all call edges, so we
+      // filter in JS. This is O(all call edges) rather than the SQL path's
+      // indexed WHERE clause. Acceptable for current data sizes; a dedicated
+      // getCallEdgesByMinConfidence(threshold) method on the Repository
+      // interface would be the proper fix if this becomes a bottleneck.
+      edges = dbOrRepo
+        .getCallEdges()
+        .filter((e) => e.confidence != null && e.confidence >= minConfidence);
+    } else {
+      edges = dbOrRepo
+        .prepare("SELECT source_id, target_id FROM edges WHERE kind = 'calls' AND confidence >= ?")
+        .all(minConfidence);
+    }
   } else {
-    edges = getCallEdges(db);
+    edges = isRepo ? dbOrRepo.getCallEdges() : getCallEdges(dbOrRepo);
   }
 
   for (const e of edges) {