fix(core,cli): resolve workspace callees and fix flaky CI test

- Resolve workspace package symlinks to source paths in callee extraction.
  pnpm workspace links (node_modules/@scope/pkg → packages/pkg) are now
  followed via realpathSync, producing cross-package edges in the graph.
- Extract normalizeAndRelativize as a pure function for dist/ → src/,
  .d.ts → .ts, and absolute → relative path normalization.
- Filter resolved paths that are still inside node_modules (e.g. @types/node)
  to prevent external dependencies from appearing in hot paths.
- Bump flaky CI test timeout from 30s to 60s (ts-morph init is slow on
  GitHub runners).
- Clean up scratchpad: remove resolved flaky test entry.

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

Author: prosdev

.claude/scratchpad.md

@@ -22,7 +22,7 @@
 
 ## Flaky Tests
 
-- **`packages/cli/src/commands/commands.test.ts:119` — "should display indexing summary without storage size"** times out at 30s on GitHub CI runners. The test indexes files and the slower CI runner can't finish in time. Needs either a higher timeout, a smaller test fixture, or mocking the indexer. Seen on PR #17 CI run.
+(none currently tracked)
 
 ## Test Gaps
 

packages/cli/src/commands/commands.test.ts

@@ -162,6 +162,6 @@ export class Calculator {
       // Verify storage size is NOT shown (deferred to `dev stats`)
       const hasStorageSize = loggedMessages.some((msg) => msg.includes('Storage:'));
       expect(hasStorageSize).toBe(false);
-    }, 30000); // 30s timeout for indexing
+    }, 60000); // 60s timeout — ts-morph project init is slow on CI runners
   });
 });

packages/core/src/scanner/__tests__/scanner.test.ts

@@ -2,7 +2,7 @@ import * as path from 'node:path';
 import { describe, expect, it } from 'vitest';
 import { MarkdownScanner } from '../markdown';
 import { ScannerRegistry } from '../registry';
-import { TypeScriptScanner } from '../typescript';
+import { normalizeAndRelativize, TypeScriptScanner } from '../typescript';
 
 // Helper to create registry
 function createDefaultRegistry(): ScannerRegistry {
@@ -1006,3 +1006,52 @@ describe('Scanner', () => {
     });
   });
 });
+
+describe('normalizeAndRelativize', () => {
+  const repoRoot = '/Users/dev/project';
+
+  it('should replace dist/ with src/', () => {
+    expect(
+      normalizeAndRelativize('/Users/dev/project/packages/core/dist/map/index.ts', repoRoot)
+    ).toBe('packages/core/src/map/index.ts');
+  });
+
+  it('should replace .d.ts with .ts', () => {
+    expect(
+      normalizeAndRelativize('/Users/dev/project/packages/core/dist/types.d.ts', repoRoot)
+    ).toBe('packages/core/src/types.ts');
+  });
+
+  it('should replace .js with .ts', () => {
+    expect(normalizeAndRelativize('/Users/dev/project/packages/core/dist/index.js', repoRoot)).toBe(
+      'packages/core/src/index.ts'
+    );
+  });
+
+  it('should handle multiple dist/ segments', () => {
+    expect(
+      normalizeAndRelativize(
+        '/Users/dev/project/packages/core/dist/formatters/dist/utils.js',
+        repoRoot
+      )
+    ).toBe('packages/core/src/formatters/src/utils.ts');
+  });
+
+  it('should make paths relative to repoRoot', () => {
+    expect(normalizeAndRelativize('/Users/dev/project/packages/cli/src/cli.ts', repoRoot)).toBe(
+      'packages/cli/src/cli.ts'
+    );
+  });
+
+  it('should return absolute path when repoRoot is empty', () => {
+    expect(normalizeAndRelativize('/abs/packages/core/src/index.ts', '')).toBe(
+      '/abs/packages/core/src/index.ts'
+    );
+  });
+
+  it('should handle path without dist/', () => {
+    expect(normalizeAndRelativize('/Users/dev/project/packages/core/src/index.ts', repoRoot)).toBe(
+      'packages/core/src/index.ts'
+    );
+  });
+});

packages/core/src/scanner/typescript.ts

@@ -1,3 +1,4 @@
+import * as fs from 'node:fs';
 import * as path from 'node:path';
 import type { Logger } from '@prosdevlab/kero';
 import {
@@ -19,6 +20,21 @@ import {
 import { getCurrentSystemResources, getOptimalConcurrency } from '../utils/concurrency';
 import type { CalleeInfo, Document, Scanner, ScannerCapabilities } from './types';
 
+/**
+ * Normalize a resolved file path: dist/ → src/, .d.ts → .ts, absolute → relative.
+ * Pure function — no I/O.
+ */
+export function normalizeAndRelativize(filePath: string, repoRoot: string): string {
+  let normalized = filePath
+    .replaceAll('/dist/', '/src/')
+    .replace(/\.d\.ts$/, '.ts')
+    .replace(/\.js$/, '.ts');
+  if (repoRoot && normalized.startsWith(repoRoot)) {
+    normalized = path.relative(repoRoot, normalized);
+  }
+  return normalized;
+}
+
 /**
  * Enhanced TypeScript scanner using ts-morph
  * Provides type information and cross-file references
@@ -987,21 +1003,7 @@ export class TypeScriptScanner implements Scanner {
             const declSourceFile = firstDecl.getSourceFile();
             if (declSourceFile) {
               const rawPath = declSourceFile.getFilePath() as string;
-              // Only include if it's within the project (not node_modules)
-              if (rawPath && !rawPath.includes('node_modules')) {
-                // Normalize: dist/ → src/, .d.ts → .ts, then make relative to repo root.
-                // ts-morph resolves imports to absolute dist output paths
-                // (e.g. /abs/packages/logger/dist/types.d.ts) but we store
-                // relative source paths (packages/logger/src/types.ts).
-                let normalized = rawPath
-                  .replaceAll('/dist/', '/src/')
-                  .replace(/\.d\.ts$/, '.ts')
-                  .replace(/\.js$/, '.ts');
-                if (this.repoRoot && normalized.startsWith(this.repoRoot)) {
-                  normalized = path.relative(this.repoRoot, normalized);
-                }
-                file = normalized;
-              }
+              file = this.normalizeCalleePath(rawPath);
             }
           }
         }
@@ -1016,4 +1018,39 @@ export class TypeScriptScanner implements Scanner {
       file,
     };
   }
+
+  /**
+   * Normalize a callee file path to a relative source path.
+   *
+   * Handles three cases:
+   * 1. Direct project files (not in node_modules) — normalize dist/ → src/
+   * 2. Workspace package symlinks (node_modules/@scope/pkg → packages/pkg) — resolve symlink
+   * 3. External node_modules — skip (return undefined)
+   */
+  private normalizeCalleePath(rawPath: string): string | undefined {
+    if (!rawPath) return undefined;
+
+    // Case 1: Not in node_modules — direct project file
+    if (!rawPath.includes('node_modules')) {
+      return normalizeAndRelativize(rawPath, this.repoRoot);
+    }
+
+    // Case 2: Workspace package symlink — resolve to real path
+    // pnpm workspace links: node_modules/@scope/pkg → ../../actual-pkg
+    // After resolving, the real path is inside the repo but NOT in node_modules
+    if (this.repoRoot) {
+      try {
+        const realPath = fs.realpathSync(rawPath);
+        if (realPath.startsWith(this.repoRoot) && !realPath.includes('node_modules')) {
+          // It's a workspace package — normalize and make relative
+          return normalizeAndRelativize(realPath, this.repoRoot);
+        }
+      } catch {
+        // realpathSync can fail if the file doesn't exist
+      }
+    }
+
+    // Case 3: External dependency — skip
+    return undefined;
+  }
 }