@optave/codegraph 3.13.0 → 3.15.0

package/src/mcp/tools/cfg.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'cfg';
 

package/src/mcp/tools/check.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'check';
 

package/src/mcp/tools/co-changes.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'co_changes';
 

package/src/mcp/tools/code-owners.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'code_owners';
 

package/src/mcp/tools/communities.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'communities';
 

package/src/mcp/tools/complexity.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'complexity';
 

package/src/mcp/tools/context.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'context';
 

package/src/mcp/tools/dataflow.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'dataflow';
 

package/src/mcp/tools/diff-impact.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'diff_impact';
 

package/src/mcp/tools/execution-flow.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'execution_flow';
 

package/src/mcp/tools/export-graph.ts

@@ -1,6 +1,6 @@
 import { findDbPath } from '../../db/index.js';
 import { effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'export_graph';
 

package/src/mcp/tools/file-deps.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'file_deps';
 

package/src/mcp/tools/file-exports.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'file_exports';
 

package/src/mcp/tools/find-cycles.ts

@@ -1,6 +1,6 @@
 import { findDbPath } from '../../db/index.js';
 import { findCycles } from '../../domain/graph/cycles.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'find_cycles';
 

package/src/mcp/tools/fn-impact.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'fn_impact';
 

package/src/mcp/tools/impact-analysis.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'impact_analysis';
 

package/src/mcp/tools/implementations.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'implementations';
 

package/src/mcp/tools/index.ts

@@ -2,12 +2,9 @@
  * Barrel module — registers all MCP tool handlers.
  */
 
-import type { McpToolContext } from '../server.js';
+import type { McpToolHandler } from '../types.js';
 
-export interface McpToolHandler {
-  name: string;
-  handler(args: any, ctx: McpToolContext): Promise<unknown>;
-}
+export type { McpToolContext, McpToolHandler } from '../types.js';
 
 import * as astQuery from './ast-query.js';
 import * as audit from './audit.js';

package/src/mcp/tools/interfaces.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'interfaces';
 

package/src/mcp/tools/list-functions.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'list_functions';
 

package/src/mcp/tools/list-repos.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'list_repos';
 

package/src/mcp/tools/module-map.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'module_map';
 

package/src/mcp/tools/node-roles.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'node_roles';
 

package/src/mcp/tools/path.ts

@@ -1,4 +1,4 @@
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'path';
 

package/src/mcp/tools/query.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'query';
 

package/src/mcp/tools/semantic-search.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'semantic_search';
 

package/src/mcp/tools/sequence.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'sequence';
 

package/src/mcp/tools/structure.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'structure';
 

package/src/mcp/tools/symbol-children.ts

@@ -1,5 +1,5 @@
 import { effectiveOffset, MCP_DEFAULTS } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'symbol_children';
 

package/src/mcp/tools/triage.ts

@@ -1,6 +1,6 @@
 import type { Role } from '../../types.js';
 import { effectiveLimit, effectiveOffset, MCP_DEFAULTS, MCP_MAX_LIMIT } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'triage';
 

package/src/mcp/tools/where.ts

@@ -1,5 +1,5 @@
 import { effectiveLimit, effectiveOffset } from '../middleware.js';
-import type { McpToolContext } from '../server.js';
+import type { McpToolContext } from '../types.js';
 
 export const name = 'where';
 

package/src/mcp/types.ts

@@ -0,0 +1,21 @@
+/**
+ * Shared MCP types used by server.ts and all tool modules.
+ * Extracted here to break the circular dependency between server.ts and tools/index.ts.
+ */
+
+import type Database from 'better-sqlite3';
+import type { findDbPath } from '../db/index.js';
+
+export interface McpToolContext {
+  dbPath: string | undefined;
+  getQueries(): Promise<any>;
+  getDatabase(): typeof Database;
+  findDbPath: typeof findDbPath;
+  allowedRepos: string[] | undefined;
+  MCP_MAX_LIMIT: number;
+}
+
+export interface McpToolHandler {
+  name: string;
+  handler(args: any, ctx: McpToolContext): Promise<unknown>;
+}

package/src/presentation/queries-cli/index.ts

@@ -9,5 +9,5 @@ export {
   queryName,
   where,
 } from './inspect.js';
-export { moduleMap, roles, stats } from './overview.js';
+export { dynamicCalls, moduleMap, roles, stats } from './overview.js';
 export { symbolPath } from './path.js';

package/src/presentation/queries-cli/overview.ts

@@ -1,5 +1,11 @@
 import path from 'node:path';
-import { kindIcon, moduleMapData, rolesData, statsData } from '../../domain/queries.js';
+import {
+  dynamicCallsData,
+  kindIcon,
+  moduleMapData,
+  rolesData,
+  statsData,
+} from '../../domain/queries.js';
 import { debug } from '../../infrastructure/logger.js';
 import { outputResult } from '../../infrastructure/result-formatter.js';
 import { toErrorMessage } from '../../shared/errors.js';
@@ -317,6 +323,34 @@ function printRoleGroup(role: string, symbols: RoleSymbol[]): void {
   console.log();
 }
 
+export function dynamicCalls(customDbPath: string, opts: OutputOpts = {}): void {
+  const rows = dynamicCallsData(customDbPath);
+  if (opts.json || opts.ndjson) {
+    outputResult(
+      { dynamic_calls: rows } as unknown as Record<string, unknown>,
+      'dynamic_calls',
+      opts,
+    );
+    return;
+  }
+  if (rows.length === 0) {
+    console.log(
+      'No flagged dynamic calls found. Run "codegraph build" first, or add JavaScript files with eval/computed-key patterns.',
+    );
+    return;
+  }
+  console.log('\nFlagged dynamic calls (confidence=0.0 sink edges):\n');
+  const total = rows.reduce((s, r) => s + r.count, 0);
+  for (const { dynamic_kind, count } of rows) {
+    const bar = '█'.repeat(Math.min(30, Math.round((count / total) * 30)));
+    console.log(`  ${dynamic_kind.padEnd(20)} ${String(count).padStart(5)}  ${bar}`);
+  }
+  console.log(`\n  Total flagged: ${total}\n`);
+  console.log(
+    '  Kinds: eval — undecidable; computed-key — obj[var](); unresolved-dynamic — other\n',
+  );
+}
+
 export function roles(customDbPath: string, opts: OutputOpts = {}): void {
   const data = rolesData(customDbPath, opts) as RolesData;
   if (outputResult(data as unknown as Record<string, unknown>, 'symbols', opts)) return;

package/src/presentation/queries-cli.ts

@@ -12,6 +12,7 @@ export {
   children,
   context,
   diffImpact,
+  dynamicCalls,
   explain,
   fileDeps,
   fileExports,

package/src/presentation/viewer.ts

@@ -150,80 +150,10 @@ export function buildLayoutOptions(cfg: PlotConfig): LayoutOptions {
   return opts;
 }
 
-// ─── HTML Renderer ───────────────────────────────────────────────────
-
-export interface ViewerNode {
-  id: number | string;
-  label: string;
-  kind: string;
-  file: string;
-  line: number;
-  role: string | null;
-  fanIn: number;
-  fanOut: number;
-  cognitive: number | null;
-  cyclomatic: number | null;
-  maintainabilityIndex: number | null;
-  community: number | null;
-  directory: string | null;
-  risk: string[];
-}
-
-export interface ViewerEdge {
-  id: number | string;
-  from: number | string;
-  to: number | string;
-}
-
-export interface ViewerData {
-  nodes: ViewerNode[];
-  edges: ViewerEdge[];
-  seedNodeIds: (number | string)[];
-}
-
-interface ResolvedPlotConfig {
-  layoutOpts: LayoutOptions;
-  title: string;
-  layoutAlgorithm: string;
-  layoutDirection: string;
-  physicsEnabled: boolean;
-  sizeBy: string;
-  clusterBy: string;
-  effectiveColorBy: string;
-  effectiveRisk: boolean;
-}
+// ─── HTML Section Renderers ──────────────────────────────────────────
 
-function resolvePlotConfig(cfg: PlotConfig): ResolvedPlotConfig {
-  return {
-    layoutOpts: buildLayoutOptions(cfg),
-    title: cfg.title || 'Codegraph',
-    layoutAlgorithm: cfg.layout?.algorithm || 'hierarchical',
-    layoutDirection: cfg.layout?.direction || 'LR',
-    physicsEnabled: cfg.physics?.enabled !== false,
-    sizeBy: cfg.sizeBy || 'uniform',
-    clusterBy: cfg.clusterBy || 'none',
-    effectiveColorBy:
-      cfg.overlays?.complexity && cfg.colorBy === 'kind' ? 'complexity' : cfg.colorBy || 'kind',
-    effectiveRisk: cfg.overlays?.risk || false,
-  };
-}
-
-export function renderPlotHTML(data: ViewerData, cfg: PlotConfig): string {
-  const {
-    layoutOpts,
-    title,
-    layoutAlgorithm,
-    layoutDirection,
-    physicsEnabled,
-    sizeBy,
-    clusterBy,
-    effectiveColorBy,
-    effectiveRisk,
-  } = resolvePlotConfig(cfg);
-
-  return `<!DOCTYPE html>
-<html lang="en">
-<head>
+function renderViewerHead(title: string): string {
+  return `<head>
 <meta charset="UTF-8">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">
 <title>${escapeHtml(title)}</title>
@@ -257,9 +187,13 @@ export function renderPlotHTML(data: ViewerData, cfg: PlotConfig): string {
   #legend div { display: flex; align-items: center; gap: 6px; margin: 2px 0; }
   #legend span.swatch { width: 14px; height: 14px; border-radius: 3px; display: inline-block; flex-shrink: 0; }
 </style>
-</head>
-<body>
-<div id="controls">
+</head>`;
+}
+
+function renderViewerControls(resolved: ResolvedPlotConfig): string {
+  const { layoutAlgorithm, physicsEnabled, effectiveColorBy, sizeBy, clusterBy, effectiveRisk } =
+    resolved;
+  return `<div id="controls">
   <label>Layout:
     <select id="layoutSelect">
       <option value="hierarchical"${layoutAlgorithm === 'hierarchical' ? ' selected' : ''}>Hierarchical</option>
@@ -293,16 +227,16 @@ export function renderPlotHTML(data: ViewerData, cfg: PlotConfig): string {
     </select>
   </label>
   <label>Risk: <input type="checkbox" id="riskToggle"${effectiveRisk ? ' checked' : ''}></label>
-</div>
-<div id="main">
-  <div id="graph"></div>
-  <div id="detail">
-    <span id="detailClose">&times;</span>
-    <div id="detailContent"></div>
-  </div>
-</div>
-<div id="legend"></div>
-<script>
+</div>`;
+}
+
+function renderViewerScript(
+  data: ViewerData,
+  cfg: PlotConfig,
+  resolved: ResolvedPlotConfig,
+): string {
+  const { layoutOpts, layoutDirection, clusterBy, effectiveColorBy } = resolved;
+  return `<script>
 /* ── Data ──────────────────────────────────────────────────────────── */
 var allNodes = ${JSON.stringify(data.nodes)};
 var allEdges = ${JSON.stringify(data.edges)};
@@ -698,7 +632,84 @@ document.getElementById('detailClose').addEventListener('click', hideDetail);
 refreshNodeAppearance();
 updateLegend(${JSON.stringify(effectiveColorBy)});
 ${clusterBy !== 'none' ? `applyClusterBy(${JSON.stringify(clusterBy)});` : ''}
-</script>
+</script>`;
+}
+
+// ─── HTML Renderer ───────────────────────────────────────────────────
+
+export interface ViewerNode {
+  id: number | string;
+  label: string;
+  kind: string;
+  file: string;
+  line: number;
+  role: string | null;
+  fanIn: number;
+  fanOut: number;
+  cognitive: number | null;
+  cyclomatic: number | null;
+  maintainabilityIndex: number | null;
+  community: number | null;
+  directory: string | null;
+  risk: string[];
+}
+
+export interface ViewerEdge {
+  id: number | string;
+  from: number | string;
+  to: number | string;
+}
+
+export interface ViewerData {
+  nodes: ViewerNode[];
+  edges: ViewerEdge[];
+  seedNodeIds: (number | string)[];
+}
+
+interface ResolvedPlotConfig {
+  layoutOpts: LayoutOptions;
+  title: string;
+  layoutAlgorithm: string;
+  layoutDirection: string;
+  physicsEnabled: boolean;
+  sizeBy: string;
+  clusterBy: string;
+  effectiveColorBy: string;
+  effectiveRisk: boolean;
+}
+
+function resolvePlotConfig(cfg: PlotConfig): ResolvedPlotConfig {
+  return {
+    layoutOpts: buildLayoutOptions(cfg),
+    title: cfg.title || 'Codegraph',
+    layoutAlgorithm: cfg.layout?.algorithm || 'hierarchical',
+    layoutDirection: cfg.layout?.direction || 'LR',
+    physicsEnabled: cfg.physics?.enabled !== false,
+    sizeBy: cfg.sizeBy || 'uniform',
+    clusterBy: cfg.clusterBy || 'none',
+    effectiveColorBy:
+      cfg.overlays?.complexity && cfg.colorBy === 'kind' ? 'complexity' : cfg.colorBy || 'kind',
+    effectiveRisk: cfg.overlays?.risk || false,
+  };
+}
+
+export function renderPlotHTML(data: ViewerData, cfg: PlotConfig): string {
+  const resolved = resolvePlotConfig(cfg);
+  const { title } = resolved;
+  return `<!DOCTYPE html>
+<html lang="en">
+${renderViewerHead(title)}
+<body>
+${renderViewerControls(resolved)}
+<div id="main">
+  <div id="graph"></div>
+  <div id="detail">
+    <span id="detailClose">&times;</span>
+    <div id="detailContent"></div>
+  </div>
+</div>
+<div id="legend"></div>
+${renderViewerScript(data, cfg, resolved)}
 </body>
 </html>`;
 }

package/src/shared/constants.ts

@@ -34,8 +34,34 @@ export const IGNORE_DIRS: ArrayCompatSet<string> = withArrayCompat(
   ]),
 );
 
+/**
+ * Merge the global IGNORE_DIRS set with a per-repo additional list from config.
+ * Returns a new Set — does not mutate IGNORE_DIRS.
+ */
+export function buildIgnoreSet(additionalDirs?: string[]): ReadonlySet<string> {
+  if (!additionalDirs || additionalDirs.length === 0) return IGNORE_DIRS;
+  return new Set([...IGNORE_DIRS, ...additionalDirs]);
+}
+
 export const EXTENSIONS: ArrayCompatSet<string> = withArrayCompat(new Set(SUPPORTED_EXTENSIONS));
 
+/**
+ * Minimum confidence assigned to resolved `ts-native` call edges.
+ *
+ * The native engine's proximity heuristic returns 0.3 for cross-module calls
+ * where no import-path evidence is available.  For ts-native edges the engine
+ * performed actual name-based symbol lookup, which is stronger evidence than
+ * pure file-proximity.  Clamping to 0.5 (same-parent-directory level) avoids
+ * unfairly dragging down the call-confidence metric.  Sink edges
+ * (confidence = 0.0) are intentionally excluded and must remain at 0.0 so
+ * they stay below DEFAULT_MIN_CONFIDENCE and never surface in normal queries.
+ *
+ * Used in `build-edges.ts` (in-memory + `applyEdgeTechniquesAfterNativeInsert`)
+ * and `native-orchestrator.ts` (`backfillEdgeTechniquesAfterNativeOrchestrator`).
+ * Centralised here so all three insertion paths apply the same value.
+ */
+export const TS_NATIVE_CONFIDENCE_FLOOR = 0.5;
+
 export function shouldIgnore(dirName: string): boolean {
   return IGNORE_DIRS.has(dirName) || dirName.startsWith('.');
 }

package/src/shared/normalize.ts

@@ -29,29 +29,20 @@ export function toSymbolRef(row: { name: string; kind: string; file: string; lin
   return { name: row.name, kind: row.kind, file: row.file, line: row.line };
 }
 
+const KIND_ICONS: Readonly<Record<string, string>> = {
+  function: 'f',
+  class: '*',
+  method: 'o',
+  file: '#',
+  interface: 'I',
+  type: 'T',
+  parameter: 'p',
+  property: '.',
+  constant: 'C',
+};
+
 export function kindIcon(kind: string): string {
-  switch (kind) {
-    case 'function':
-      return 'f';
-    case 'class':
-      return '*';
-    case 'method':
-      return 'o';
-    case 'file':
-      return '#';
-    case 'interface':
-      return 'I';
-    case 'type':
-      return 'T';
-    case 'parameter':
-      return 'p';
-    case 'property':
-      return '.';
-    case 'constant':
-      return 'C';
-    default:
-      return '-';
-  }
+  return KIND_ICONS[kind] ?? '-';
 }
 
 export interface NormalizedSymbol {