@monoes/monograph 1.2.10 → 1.3.0

package/src/pipeline/phases/scope-resolution.ts

@@ -1,5 +1,5 @@
-import { readFileSync } from 'fs';
-import { join, extname } from 'path';
+import { readFileSync, existsSync } from 'fs';
+import { join, extname, dirname, resolve as resolvePath } from 'path';
 import type { PipelinePhase, PipelineContext } from '../types.js';
 import type { MonographNode } from '../../types.js';
 import { makeId } from '../../types.js';
@@ -11,6 +11,9 @@ export interface ScopeResolutionOutput {
   resolvedEdges: number;
   skippedDynamic: number;
   ambiguous: number;
+  reexportEdges: number;
+  orphanImportsRemoved: number;
+  importsReconstructed: number;
 }
 
 // ── Call site ─────────────────────────────────────────────────────────────────
@@ -68,8 +71,10 @@ const GO_EXTS = new Set(['.go']);
 const JAVA_EXTS = new Set(['.java']);
 const RUST_EXTS = new Set(['.rs']);
 
+const CJS_MJS_EXTS = new Set(['.cjs', '.mjs']);
+
 function isSupportedExt(ext: string): boolean {
-  return TS_JS_EXTS.has(ext) || PY_EXTS.has(ext) || GO_EXTS.has(ext) || JAVA_EXTS.has(ext) || RUST_EXTS.has(ext);
+  return TS_JS_EXTS.has(ext) || CJS_MJS_EXTS.has(ext) || PY_EXTS.has(ext) || GO_EXTS.has(ext) || JAVA_EXTS.has(ext) || RUST_EXTS.has(ext);
 }
 
 // ── Language-specific extractors ──────────────────────────────────────────────
@@ -122,6 +127,22 @@ export function extractRustCallSites(source: string, filePath: string, fileNodeI
   return sites;
 }
 
+// ── Stage 0.5: Track constructor assignments for type-aware method resolution ─
+
+/**
+ * Scan source for `const/let/var x = new ClassName(...)` patterns.
+ * Returns a map: localVarName → ClassName (e.g. "svc" → "MyService").
+ */
+function extractConstructorAssignments(source: string): Map<string, string> {
+  const result = new Map<string, string>();
+  const pattern = /(?:const|let|var)\s+(\w+)\s*=\s*new\s+([A-Z][\w$]*)\s*(?:<[^>]*>\s*)?\(/g;
+  let m: RegExpExecArray | null;
+  while ((m = pattern.exec(source)) !== null) {
+    result.set(m[1], m[2]);
+  }
+  return result;
+}
+
 // ── Stage 1 + 2: Extract and classify call sites ──────────────────────────────
 
 function extractCallSites(
@@ -132,9 +153,9 @@ function extractCallSites(
 ): CallSite[] {
   const sites: CallSite[] = [];
 
-  if (TS_JS_EXTS.has(ext)) {
-    // Method calls: word.word(
-    const methodPattern = /(\w+)\.(\w+)\s*\(/g;
+  if (TS_JS_EXTS.has(ext) || CJS_MJS_EXTS.has(ext)) {
+    // Method calls: word.word( or word.word<T>(
+    const methodPattern = /(\w+)\.(\w+)\s*(?:<[^>]*>\s*)?\(/g;
     let m: RegExpExecArray | null;
     while ((m = methodPattern.exec(source)) !== null) {
       sites.push({
@@ -147,8 +168,22 @@ function extractCallSites(
       });
     }
 
-    // Direct calls: word( not preceded by . or word char
-    const directPattern = /(?<![.[\w])([A-Za-z_$][\w$]*)\s*\(/g;
+    // Chained method calls: ).method( or ].method( — receiver unknown, resolve by method name
+    const chainedPattern = /[)\]]\s*\.(\w+)\s*(?:<[^>]*>\s*)?\(/g;
+    while ((m = chainedPattern.exec(source)) !== null) {
+      const name = m[1];
+      if (JS_KEYWORDS.has(name)) continue;
+      sites.push({
+        callerFileNodeId: fileNodeId,
+        callerFilePath: filePath,
+        calleeRaw: `?.${name}`,
+        form: 'method',
+        methodName: name,
+      });
+    }
+
+    // Direct calls: word( or word<T>( — not preceded by . or word char
+    const directPattern = /(?<![.[\w])([A-Za-z_$][\w$]*)\s*(?:<[^>]*>\s*)?\(/g;
     while ((m = directPattern.exec(source)) !== null) {
       const name = m[1];
       if (JS_KEYWORDS.has(name)) continue;
@@ -161,6 +196,18 @@ function extractCallSites(
       });
     }
 
+    // Constructor calls: new ClassName( or new ClassName<T>(
+    const newPattern = /\bnew\s+([A-Z][\w$]*)\s*(?:<[^>]*>\s*)?\(/g;
+    while ((m = newPattern.exec(source)) !== null) {
+      sites.push({
+        callerFileNodeId: fileNodeId,
+        callerFilePath: filePath,
+        calleeRaw: `new ${m[1]}`,
+        form: 'direct',
+        methodName: m[1],
+      });
+    }
+
     // Dynamic calls: obj[key]( → mark as dynamic
     const dynamicPattern = /\w+\s*\[[\w'"` ]+\]\s*\(/g;
     while ((m = dynamicPattern.exec(source)) !== null) {
@@ -210,53 +257,312 @@ function extractCallSites(
   return sites;
 }
 
-// ── Stage 3: Build import maps from DB (batch) ────────────────────────────────
+// ── Stage 3: Build import maps by parsing source imports ─────────────────────
+
+const IMPORT_RE = /import\s+(?:type\s+)?(?:\{([^}]+)\}|(\w+)|\*\s+as\s+(\w+))(?:\s*,\s*(?:\{([^}]+)\}|(\w+)|\*\s+as\s+(\w+)))?\s+from\s+['"]([^'"]+)['"]/g;
+
+// CJS require: const x = require('y') or const { a, b } = require('y')
+const REQUIRE_RE = /(?:const|let|var)\s+(?:\{([^}]+)\}|(\w+))\s*=\s*require\s*\(\s*['"]([^'"]+)['"]\s*\)/g;
+
+// Python: from x import y, z  OR  import x
+const PY_FROM_IMPORT_RE = /from\s+([\w.]+)\s+import\s+(.+)/g;
+const PY_IMPORT_RE = /^import\s+([\w.]+)(?:\s+as\s+(\w+))?/gm;
+
+// Go: import "path" or import ( "path" )
+const GO_IMPORT_RE = /import\s+(?:"([^"]+)"|(?:\w+\s+)?"([^"]+)"|\(\s*([\s\S]*?)\s*\))/g;
+
+// Java: import com.foo.Bar;
+const JAVA_IMPORT_RE = /import\s+(?:static\s+)?([\w.]+)\s*;/g;
+
+// Rust: use crate::module::Item; or use super::foo;
+const RUST_USE_RE = /use\s+((?:crate|super|self)(?:::\w+)+)(?:::\{([^}]+)\})?;/g;
+
+// TS/JS re-exports: export { foo, bar } from './module'
+const REEXPORT_RE = /export\s+\{([^}]+)\}\s+from\s+['"]([^'"]+)['"]/g;
+
+const RESOLVE_EXTS = ['.ts', '.tsx', '.js', '.jsx'];
+const PY_RESOLVE_EXTS = ['.py'];
+const GO_RESOLVE_EXTS = ['.go'];
+const JAVA_RESOLVE_EXTS = ['.java'];
+const RUST_RESOLVE_EXTS = ['.rs'];
+
+/**
+ * Build package-name → directory map from workspace package.json files.
+ * Scans packages/ for package.json and maps npm name to its relative src path.
+ */
+function buildWorkspacePackageMap(repoPath: string): Map<string, string> {
+  const result = new Map<string, string>();
+  const packagesDir = join(repoPath, 'packages');
+  try {
+    const scanDirs = (base: string, depth: number) => {
+      if (depth > 2) return;
+      let entries: string[];
+      try { entries = require('fs').readdirSync(base); } catch { return; }
+      for (const e of entries) {
+        const full = join(base, e);
+        const pkgJson = join(full, 'package.json');
+        try {
+          const pkg = JSON.parse(readFileSync(pkgJson, 'utf-8'));
+          if (pkg.name) {
+            const relDir = full.slice(repoPath.length + 1); // e.g. packages/@monomind/cli
+            result.set(pkg.name, relDir);
+          }
+        } catch {
+          // No package.json — recurse for @scoped dirs
+          if (e.startsWith('@')) scanDirs(full, depth + 1);
+        }
+      }
+    };
+    scanDirs(packagesDir, 0);
+  } catch { /* no packages dir */ }
+  return result;
+}
+
+function resolveModuleSpecifier(
+  importerPath: string,
+  specifier: string,
+  repoPath: string,
+  knownFiles: Set<string>,
+  workspaceMap: Map<string, string>,
+): string | null {
+  if (specifier.startsWith('.')) {
+    const dir = dirname(importerPath);
+    const raw = resolvePath('/', dir, specifier).slice(1);
+    // Strip .js/.jsx — TS source uses .js extensions but files are .ts
+    const base = raw.replace(/\.(js|jsx)$/, '');
+
+    for (const candidate of [
+      raw,
+      base,
+      ...RESOLVE_EXTS.map(e => base + e),
+      ...RESOLVE_EXTS.map(e => base + '/index' + e),
+    ]) {
+      if (knownFiles.has(candidate)) return candidate;
+    }
+
+    for (const ext of RESOLVE_EXTS) {
+      if (existsSync(join(repoPath, base + ext))) return base + ext;
+    }
+    return null;
+  }
+
+  // Workspace package specifier: @monomind/hooks → packages/@monomind/hooks/src/index.ts
+  // Also handles subpath: @monomind/hooks/src/foo → packages/@monomind/hooks/src/foo.ts
+  for (const [pkgName, pkgDir] of workspaceMap) {
+    if (specifier === pkgName) {
+      // Bare import: resolve to package entry point (src/index.ts)
+      for (const entry of RESOLVE_EXTS.map(e => pkgDir + '/src/index' + e)) {
+        if (knownFiles.has(entry)) return entry;
+      }
+      return null;
+    }
+    if (specifier.startsWith(pkgName + '/')) {
+      const subpath = specifier.slice(pkgName.length + 1);
+      const base = pkgDir + '/' + subpath;
+      for (const candidate of [
+        base,
+        ...RESOLVE_EXTS.map(e => base + e),
+        ...RESOLVE_EXTS.map(e => base + '/index' + e),
+      ]) {
+        if (knownFiles.has(candidate)) return candidate;
+      }
+      return null;
+    }
+  }
+
+  return null;
+}
+
+function resolvePythonModule(importerPath: string, modulePath: string, knownFiles: Set<string>): string | null {
+  // Try relative to importer's directory, then absolute from repo root
+  const dir = dirname(importerPath);
+  for (const base of [dir + '/' + modulePath, modulePath]) {
+    for (const candidate of [base + '.py', base + '/__init__.py']) {
+      if (knownFiles.has(candidate)) return candidate;
+    }
+  }
+  return null;
+}
+
+function resolveGoPackage(importerPath: string, goPath: string, knownFiles: Set<string>): string | null {
+  for (const f of knownFiles) {
+    if (f.startsWith(goPath + '/') && f.endsWith('.go')) return f;
+  }
+  return null;
+}
+
+function resolveJavaImport(qualifiedName: string, knownFiles: Set<string>): string | null {
+  // com.foo.Bar → com/foo/Bar.java or src/main/java/com/foo/Bar.java
+  const pathPart = qualifiedName.replace(/\./g, '/');
+  for (const candidate of [pathPart + '.java', 'src/main/java/' + pathPart + '.java', 'src/' + pathPart + '.java']) {
+    if (knownFiles.has(candidate)) return candidate;
+  }
+  // Wildcard: com.foo.* → find any .java file in com/foo/
+  if (pathPart.endsWith('/*')) {
+    const dir = pathPart.slice(0, -2);
+    for (const f of knownFiles) {
+      if (f.endsWith('.java') && (f.startsWith(dir + '/') || f.includes('/' + dir + '/'))) return f;
+    }
+  }
+  return null;
+}
+
+function resolveRustUse(usePath: string, importerPath: string, knownFiles: Set<string>): string | null {
+  // crate::module::item → src/module.rs or src/module/mod.rs
+  const parts = usePath.split('::');
+  if (parts[0] === 'crate') parts[0] = 'src';
+  else if (parts[0] === 'super') {
+    const dir = dirname(importerPath);
+    parts[0] = dirname(dir);
+  } else if (parts[0] === 'self') {
+    parts[0] = dirname(importerPath);
+  }
+  // Last segment is the item name — try with and without it
+  for (let len = parts.length; len >= 2; len--) {
+    const base = parts.slice(0, len).join('/');
+    for (const candidate of [base + '.rs', base + '/mod.rs']) {
+      if (knownFiles.has(candidate)) return candidate;
+    }
+  }
+  return null;
+}
+
+function extractImportNames(clause: string): string[] {
+  return clause
+    .split(',')
+    .map(s => s.trim().split(/\s+as\s+/).pop()!.trim())
+    .filter(Boolean);
+}
 
 /**
- * Load all IMPORTS edges once and return a map of fileNodeId → (name → filePath).
- * Eliminates the N+1 pattern of querying per-file inside the main loop.
+ * Parse each file's import statements to build importedName → resolvedFilePath maps.
+ * Replaces the broken DB-edge approach (IMPORTS edges target Variable nodes, not Files).
  */
-function buildAllImportMaps(
-  ctx: PipelineContext,
-  symbolNodes: MonographNode[],
+function buildAllImportMapsFromSource(
+  repoPath: string,
+  fileNodesByPath: Map<string, MonographNode>,
+  fileContents?: Map<string, string>,
 ): Map<string, Map<string, string>> {
   const result = new Map<string, Map<string, string>>();
-  if (!ctx.db) return result;
-
-  // Build a lookup: fileNodeId → filePath from symbolNodes
-  const idToFilePath = new Map<string, string>();
-  for (const n of symbolNodes) {
-    if (n.label === 'File' && n.filePath) {
-      idToFilePath.set(n.id, n.filePath);
-      // Also register the alternate makeId form
-      const altId = makeId(n.filePath.replace(/\//g, '_'), 'file');
-      if (altId !== n.id) idToFilePath.set(altId, n.filePath);
+  const knownFiles = new Set(fileNodesByPath.keys());
+  const workspaceMap = buildWorkspacePackageMap(repoPath);
+
+  for (const [filePath, fileNode] of fileNodesByPath) {
+    const ext = extname(filePath).toLowerCase();
+    const importMap = new Map<string, string>();
+
+    let source: string | undefined = fileContents?.get(filePath);
+    if (!source) {
+      try {
+        source = readFileSync(join(repoPath, filePath), 'utf-8');
+      } catch {
+        continue;
+      }
     }
-  }
 
-  // Load ALL IMPORTS edges in one query
-  const importsRows = ctx.db
-    .prepare(`SELECT source_id, target_id FROM edges WHERE relation = 'IMPORTS'`)
-    .all() as { source_id: string; target_id: string }[];
+    if (TS_JS_EXTS.has(ext) || ext === '.cjs' || ext === '.mjs') {
+      // ESM imports
+      IMPORT_RE.lastIndex = 0;
+      let m: RegExpExecArray | null;
+      while ((m = IMPORT_RE.exec(source)) !== null) {
+        const specifier = m[7];
+        const resolved = resolveModuleSpecifier(filePath, specifier, repoPath, knownFiles, workspaceMap);
+        if (!resolved) continue;
+
+        if (m[1]) for (const n of extractImportNames(m[1])) importMap.set(n, resolved);
+        if (m[4]) for (const n of extractImportNames(m[4])) importMap.set(n, resolved);
+        if (m[2]) importMap.set(m[2], resolved);
+        if (m[5]) importMap.set(m[5], resolved);
+        if (m[3]) importMap.set(m[3], resolved);
+        if (m[6]) importMap.set(m[6], resolved);
+        const baseName = resolved.split('/').pop()!.replace(/\.\w+$/, '');
+        importMap.set(baseName, resolved);
+      }
+
+      // CJS require()
+      REQUIRE_RE.lastIndex = 0;
+      while ((m = REQUIRE_RE.exec(source)) !== null) {
+        const specifier = m[3];
+        const resolved = resolveModuleSpecifier(filePath, specifier, repoPath, knownFiles, workspaceMap);
+        if (!resolved) continue;
+        if (m[1]) for (const n of extractImportNames(m[1])) importMap.set(n, resolved);
+        if (m[2]) importMap.set(m[2], resolved);
+        const baseName = resolved.split('/').pop()!.replace(/\.\w+$/, '');
+        importMap.set(baseName, resolved);
+      }
+    } else if (PY_EXTS.has(ext)) {
+      // Python: from module import name
+      PY_FROM_IMPORT_RE.lastIndex = 0;
+      let m: RegExpExecArray | null;
+      while ((m = PY_FROM_IMPORT_RE.exec(source)) !== null) {
+        const modulePath = m[1].replace(/\./g, '/');
+        const resolved = resolvePythonModule(filePath, modulePath, knownFiles);
+        if (!resolved) continue;
+        for (const name of m[2].split(',').map(s => s.trim().split(/\s+as\s+/).pop()!.trim()).filter(Boolean)) {
+          importMap.set(name, resolved);
+        }
+        const baseName = resolved.split('/').pop()!.replace(/\.\w+$/, '');
+        importMap.set(baseName, resolved);
+      }
+      // Python: import module
+      PY_IMPORT_RE.lastIndex = 0;
+      while ((m = PY_IMPORT_RE.exec(source)) !== null) {
+        const modulePath = m[1].replace(/\./g, '/');
+        const resolved = resolvePythonModule(filePath, modulePath, knownFiles);
+        if (!resolved) continue;
+        const alias = m[2] ?? m[1].split('.').pop()!;
+        importMap.set(alias, resolved);
+      }
+    } else if (GO_EXTS.has(ext)) {
+      GO_IMPORT_RE.lastIndex = 0;
+      let m: RegExpExecArray | null;
+      while ((m = GO_IMPORT_RE.exec(source)) !== null) {
+        const paths = m[3]
+          ? m[3].match(/"([^"]+)"/g)?.map(s => s.slice(1, -1)) ?? []
+          : [m[1] ?? m[2]].filter(Boolean);
+        for (const goPath of paths) {
+          const resolved = resolveGoPackage(filePath, goPath, knownFiles);
+          if (!resolved) continue;
+          const pkgName = goPath.split('/').pop()!;
+          importMap.set(pkgName, resolved);
+        }
+      }
+    } else if (JAVA_EXTS.has(ext)) {
+      JAVA_IMPORT_RE.lastIndex = 0;
+      let m: RegExpExecArray | null;
+      while ((m = JAVA_IMPORT_RE.exec(source)) !== null) {
+        const resolved = resolveJavaImport(m[1], knownFiles);
+        if (!resolved) continue;
+        const className = m[1].split('.').pop()!;
+        importMap.set(className, resolved);
+      }
+    } else if (RUST_EXTS.has(ext)) {
+      RUST_USE_RE.lastIndex = 0;
+      let m: RegExpExecArray | null;
+      while ((m = RUST_USE_RE.exec(source)) !== null) {
+        if (m[2]) {
+          // use crate::module::{Item1, Item2}
+          for (const name of m[2].split(',').map(s => s.trim()).filter(Boolean)) {
+            const resolved = resolveRustUse(m[1] + '::' + name, filePath, knownFiles);
+            if (resolved) importMap.set(name.split('::').pop()!, resolved);
+          }
+        } else {
+          const resolved = resolveRustUse(m[1], filePath, knownFiles);
+          if (!resolved) continue;
+          const itemName = m[1].split('::').pop()!;
+          importMap.set(itemName, resolved);
+        }
+      }
+    }
 
-  for (const row of importsRows) {
-    const targetPath = idToFilePath.get(row.target_id);
-    if (!targetPath) continue;
-    let fileMap = result.get(row.source_id);
-    if (!fileMap) {
-      fileMap = new Map();
-      result.set(row.source_id, fileMap);
+    if (importMap.size > 0) {
+      result.set(fileNode.id, importMap);
     }
-    const parts = targetPath.split('/');
-    const baseName = parts[parts.length - 1].replace(/\.\w+$/, '');
-    fileMap.set(baseName, targetPath);
-    fileMap.set(targetPath, targetPath);
   }
 
   return result;
 }
 
-/** Returns the pre-built import map for a given file node (empty map if not found). */
 function getImportMap(
   allImportMaps: Map<string, Map<string, string>>,
   fileNodeId: string,
@@ -267,10 +573,8 @@ function getImportMap(
 // ── Stage 4 helpers: preloaded function/method index ──────────────────────────
 
 /**
- * Load all Function/Method/Constructor nodes once.
- * Returns two indices:
- * - byFilePath: filePath → name → id[] (for resolveTarget candidate lookup)
- * - nameCounts: name → total occurrences across all files (for ambiguity check)
+ * Load all callable nodes once (Function, Method, Constructor, Class).
+ * Class is included so `new ClassName()` can resolve to Class nodes.
  */
 function buildFunctionIndex(ctx: PipelineContext): {
   byFilePath: Map<string, Map<string, string[]>>;
@@ -282,7 +586,7 @@ function buildFunctionIndex(ctx: PipelineContext): {
   if (!ctx.db) return { byFilePath, nameCounts };
 
   const rows = ctx.db
-    .prepare(`SELECT id, name, file_path FROM nodes WHERE label IN ('Function', 'Method', 'Constructor') AND file_path IS NOT NULL`)
+    .prepare(`SELECT id, name, file_path FROM nodes WHERE label IN ('Function', 'Method', 'Constructor', 'Class') AND file_path IS NOT NULL`)
     .all() as { id: string; name: string; file_path: string }[];
 
   for (const row of rows) {
@@ -308,11 +612,27 @@ function buildFunctionIndex(ctx: PipelineContext): {
 
 // ── Stage 4 + 5: Resolve target node (index-based, no per-call DB query) ──────
 
+function pickBestId(ids: string[], site: CallSite): string | null {
+  if (ids.length === 1) return ids[0];
+  if (ids.length === 0) return null;
+  // Disambiguate: prefer Function for direct calls, Method for method calls
+  const suffix = site.form === 'method' ? '_method' : '_function';
+  const match = ids.find(id => id.endsWith(suffix));
+  // For `new ClassName()` prefer _class
+  if (!match && site.calleeRaw.startsWith('new ')) {
+    const classMatch = ids.find(id => id.endsWith('_class'));
+    if (classMatch) return classMatch;
+  }
+  return match ?? ids[0];
+}
+
 function resolveTarget(
   site: CallSite,
   callerFilePath: string,
   importMap: Map<string, string>,
   fnIndex: Map<string, Map<string, string[]>>,
+  ctorMap: Map<string, string> | undefined,
+  importedFiles: string[],
 ): { targetId: string } | null {
   const methodName = site.methodName;
   if (!methodName) return null;
@@ -320,23 +640,44 @@ function resolveTarget(
   let candidateFilePaths: string[];
 
   if (site.form === 'method' && site.receiverName) {
-    // Stage 3: Infer receiver type — look up receiver in import map
     const receiverPath = importMap.get(site.receiverName);
-    candidateFilePaths = receiverPath ? [receiverPath] : [callerFilePath];
+    if (receiverPath) {
+      candidateFilePaths = [receiverPath];
+    } else {
+      const className = ctorMap?.get(site.receiverName);
+      const classFilePath = className ? importMap.get(className) : undefined;
+      if (classFilePath) {
+        candidateFilePaths = [classFilePath, callerFilePath];
+      } else {
+        const sameFileIds = fnIndex.get(callerFilePath)?.get(methodName);
+        if (sameFileIds && sameFileIds.length > 0) {
+          return { targetId: pickBestId(sameFileIds, site)! };
+        }
+        const matches = importedFiles.filter(fp => fnIndex.get(fp)?.has(methodName));
+        if (matches.length === 1) {
+          const ids = fnIndex.get(matches[0])!.get(methodName)!;
+          return { targetId: pickBestId(ids, site)! };
+        }
+        return null;
+      }
+    }
   } else if (site.form === 'direct') {
-    // Direct call: same file first, then all imported files
-    candidateFilePaths = [callerFilePath, ...importMap.values()];
+    const importedFrom = importMap.get(methodName);
+    if (importedFrom) {
+      candidateFilePaths = [importedFrom, callerFilePath];
+    } else {
+      candidateFilePaths = [callerFilePath, ...importedFiles];
+    }
   } else {
     return null;
   }
 
-  // Stage 5: O(1) lookup in preloaded index instead of per-call DB query
   for (const fp of candidateFilePaths) {
     const ids = fnIndex.get(fp)?.get(methodName);
-    if (ids && ids.length === 1) {
-      return { targetId: ids[0] };
+    if (ids && ids.length > 0) {
+      const best = pickBestId(ids, site);
+      if (best) return { targetId: best };
     }
-    // ids.length > 1 → ambiguous within this file — skip to next candidate
   }
 
   return null;
@@ -344,47 +685,48 @@ function resolveTarget(
 
 // ── Stage 6: Emit edge ────────────────────────────────────────────────────────
 
+interface PreparedEdgeStmts {
+  selectExisting: import('better-sqlite3').Statement;
+  updateScore: import('better-sqlite3').Statement;
+  insertNew: import('better-sqlite3').Statement;
+}
+
+function prepareEdgeStmts(db: import('better-sqlite3').Database): PreparedEdgeStmts {
+  return {
+    selectExisting: db.prepare(
+      `SELECT id, confidence_score FROM edges WHERE source_id = ? AND target_id = ? AND relation = 'CALLS'`
+    ),
+    updateScore: db.prepare(
+      `UPDATE edges SET confidence_score = ?, confidence = 'EXTRACTED' WHERE id = ?`
+    ),
+    insertNew: db.prepare(
+      `INSERT OR IGNORE INTO edges (id, source_id, target_id, relation, confidence, confidence_score) VALUES (?, ?, ?, 'CALLS', 'EXTRACTED', ?)`
+    ),
+  };
+}
+
+const RESOLVED_CONFIDENCE_SCORE = 0.75;
+
 function emitEdge(
-  ctx: PipelineContext,
+  stmts: PreparedEdgeStmts,
   sourceId: string,
   targetId: string,
 ): 'inserted' | 'upgraded' | 'skipped' {
-  if (!ctx.db) return 'skipped';
   if (sourceId === targetId) return 'skipped';
 
-  const RESOLVED_CONFIDENCE_SCORE = 0.75;
-
-  // Check if a CALLS edge already exists
-  const existing = ctx.db
-    .prepare(`
-      SELECT id, confidence_score FROM edges
-      WHERE source_id = ? AND target_id = ? AND relation = 'CALLS'
-    `)
-    .get(sourceId, targetId) as { id: string; confidence_score: number } | undefined;
+  const existing = stmts.selectExisting.get(sourceId, targetId) as { id: string; confidence_score: number } | undefined;
 
   if (existing) {
     const newScore = Math.max(existing.confidence_score, RESOLVED_CONFIDENCE_SCORE);
     if (newScore > existing.confidence_score) {
-      ctx.db
-        .prepare(`
-          UPDATE edges
-          SET confidence_score = ?, confidence = 'EXTRACTED'
-          WHERE id = ?
-        `)
-        .run(newScore, existing.id);
+      stmts.updateScore.run(newScore, existing.id);
     }
     return 'upgraded';
   }
 
-  // Insert new CALLS edge
   const edgeId = makeId(sourceId, targetId, 'calls_resolved');
   try {
-    ctx.db
-      .prepare(`
-        INSERT OR IGNORE INTO edges (id, source_id, target_id, relation, confidence, confidence_score)
-        VALUES (?, ?, ?, 'CALLS', 'EXTRACTED', ?)
-      `)
-      .run(edgeId, sourceId, targetId, RESOLVED_CONFIDENCE_SCORE);
+    stmts.insertNew.run(edgeId, sourceId, targetId, RESOLVED_CONFIDENCE_SCORE);
     return 'inserted';
   } catch {
     return 'skipped';
@@ -397,6 +739,9 @@ export const scopeResolutionPhase: PipelinePhase<ScopeResolutionOutput> = {
   name: 'scope-resolution',
   deps: ['parse', 'cross-file'],
   async execute(ctx, deps) {
+    if (ctx.allFilesCached) {
+      return { resolvedEdges: 0, skippedDynamic: 0, ambiguous: 0, reexportEdges: 0, orphanImportsRemoved: 0, importsReconstructed: 0 };
+    }
     const { symbolNodes } = deps.get('parse') as ParseOutput;
 
     let resolvedEdges = 0;
@@ -432,58 +777,156 @@ export const scopeResolutionPhase: PipelinePhase<ScopeResolutionOutput> = {
       }
     }
 
-    // Preload all IMPORTS edges → per-file import maps (one DB query total)
-    const allImportMaps = buildAllImportMaps(ctx, symbolNodes);
+    // Parse source imports → per-file import maps (replaces broken DB-edge approach)
+    const { fileContents } = deps.get('parse') as ParseOutput;
+    const allImportMaps = buildAllImportMapsFromSource(ctx.repoPath, fileNodesByPath, fileContents);
 
     // Preload all Function/Method/Constructor nodes into indices (one DB query total)
     const { byFilePath: fnIndex, nameCounts } = buildFunctionIndex(ctx);
 
-    for (const [filePath, fileNode] of fileNodesByPath) {
-      const ext = extname(filePath).toLowerCase();
-      if (!isSupportedExt(ext)) continue;
+    const edgeStmts = ctx.db ? prepareEdgeStmts(ctx.db) : null;
+    const resolveAllCalls = ctx.db?.transaction(() => {
+      for (const [filePath, fileNode] of fileNodesByPath) {
+        const ext = extname(filePath).toLowerCase();
+        if (!isSupportedExt(ext)) continue;
+
+        // Read file source (prefer cached from parse phase)
+        let source: string | undefined = fileContents.get(filePath);
+        if (!source) {
+          try {
+            source = readFileSync(join(ctx.repoPath, filePath), 'utf-8');
+          } catch {
+            continue;
+          }
+        }
 
-      // Read file source
-      let source: string;
-      try {
-        source = readFileSync(join(ctx.repoPath, filePath), 'utf-8');
-      } catch {
-        continue;
-      }
+        // Stage 1+2: Extract call sites
+        const callSites = extractCallSites(source, filePath, fileNode.id, ext);
 
-      // Stage 1+2: Extract call sites
-      const callSites = extractCallSites(source, filePath, fileNode.id, ext);
+        // Stage 3: Get pre-built import map for this file (O(1))
+        const importMap = getImportMap(allImportMaps, fileNode.id);
 
-      // Stage 3: Get pre-built import map for this file (O(1))
-      const importMap = getImportMap(allImportMaps, fileNode.id);
+        // Track constructor assignments for type-aware method resolution
+        const ctorMap = (TS_JS_EXTS.has(ext) || CJS_MJS_EXTS.has(ext)) ? extractConstructorAssignments(source) : undefined;
 
-      for (const site of callSites) {
-        if (site.form === 'dynamic') {
-          skippedDynamic++;
-          continue;
-        }
+        // Precompute once per file instead of per call site
+        const importedFiles = [...new Set(importMap.values())];
+
+        for (const site of callSites) {
+          if (site.form === 'dynamic') {
+            skippedDynamic++;
+            continue;
+          }
+
+          // Stage 4+5: Resolve target using preloaded indices (no DB query)
+          const resolved = resolveTarget(site, filePath, importMap, fnIndex, ctorMap, importedFiles);
 
-        // Stage 4+5: Resolve target using preloaded indices (no DB query)
-        const resolved = resolveTarget(site, filePath, importMap, fnIndex);
+          if (!resolved) {
+            continue;
+          }
 
-        if (!resolved) {
-          // Could not resolve — method calls with unresolvable receivers are simply skipped
-          continue;
+          // Ambiguity check using preloaded name counts (no DB query)
+          if (site.methodName && (nameCounts.get(site.methodName) ?? 0) > 1) {
+            ambiguous++;
+          }
+
+          // Stage 6: Emit edge (source is the file node of the caller)
+          const result = edgeStmts ? emitEdge(edgeStmts, site.callerFileNodeId, resolved.targetId) : 'skipped';
+          if (result === 'inserted' || result === 'upgraded') {
+            resolvedEdges++;
+          }
         }
+      }
+    });
+    resolveAllCalls?.();
 
-        // Ambiguity check using preloaded name counts (no DB query)
-        if (site.methodName && (nameCounts.get(site.methodName) ?? 0) > 1) {
-          ambiguous++;
-          // Still emit — we found exactly one candidate in the caller's context
+    // Scan for re-exports: export { foo, bar } from './module'
+    // Creates REFERENCES edges so re-exported symbols don't appear as dead code.
+    let reexportEdges = 0;
+    if (ctx.db) {
+      const insertRef = ctx.db.prepare(`
+        INSERT OR IGNORE INTO edges (id, source_id, target_id, relation, confidence, confidence_score)
+        VALUES (?, ?, ?, 'REFERENCES', 'EXTRACTED', 0.85)
+      `);
+      const insertReexports = ctx.db.transaction(() => {
+        for (const [filePath, fileNode] of fileNodesByPath) {
+          const ext = extname(filePath).toLowerCase();
+          if (!TS_JS_EXTS.has(ext) && !CJS_MJS_EXTS.has(ext)) continue;
+
+          let source: string | undefined = fileContents.get(filePath);
+          if (!source) { try { source = readFileSync(join(ctx.repoPath, filePath), 'utf-8'); } catch { continue; } }
+
+          const importMap = getImportMap(allImportMaps, fileNode.id);
+          REEXPORT_RE.lastIndex = 0;
+          let m: RegExpExecArray | null;
+          while ((m = REEXPORT_RE.exec(source)) !== null) {
+            const specifier = m[2];
+            const names = extractImportNames(m[1]);
+            // Resolve the source module
+            const knownFiles = new Set(fileNodesByPath.keys());
+            const workspaceMap = buildWorkspacePackageMap(ctx.repoPath);
+            const resolvedFile = resolveModuleSpecifier(filePath, specifier, ctx.repoPath, knownFiles, workspaceMap);
+            if (!resolvedFile) continue;
+
+            for (const name of names) {
+              // Find the function/class node in the source file
+              const ids = fnIndex.get(resolvedFile)?.get(name);
+              if (!ids || ids.length === 0) continue;
+              const targetId = ids.length === 1 ? ids[0] : (ids.find(id => id.endsWith('_function')) ?? ids[0]);
+              const edgeId = makeId(fileNode.id, targetId, 'reexport_ref');
+              try {
+                insertRef.run(edgeId, fileNode.id, targetId);
+                reexportEdges++;
+              } catch { /* duplicate */ }
+            }
+          }
         }
+      });
+      insertReexports();
+    }
 
-        // Stage 6: Emit edge (source is the file node of the caller)
-        const result = emitEdge(ctx, site.callerFileNodeId, resolved.targetId);
-        if (result === 'inserted' || result === 'upgraded') {
-          resolvedEdges++;
+    // Clean up orphan IMPORTS edges that target Variable nodes instead of Files.
+    let orphanImportsRemoved = 0;
+    if (ctx.db) {
+      const result = ctx.db
+        .prepare(`
+          DELETE FROM edges WHERE id IN (
+            SELECT e.id FROM edges e
+            JOIN nodes t ON e.target_id = t.id
+            WHERE e.relation = 'IMPORTS' AND t.label = 'Variable'
+          )
+        `)
+        .run();
+      orphanImportsRemoved = result.changes;
+    }
+
+    // Reconstruct proper File→File IMPORTS edges from source-parsed import maps.
+    let importsReconstructed = 0;
+    if (ctx.db) {
+      const insertImport = ctx.db.prepare(`
+        INSERT OR IGNORE INTO edges (id, source_id, target_id, relation, confidence, confidence_score)
+        VALUES (?, ?, ?, 'IMPORTS', 'EXTRACTED', 0.9)
+      `);
+      const fileIdByPath = new Map<string, string>();
+      for (const [fp, node] of fileNodesByPath) fileIdByPath.set(fp, node.id);
+
+      const insertAll = ctx.db.transaction(() => {
+        for (const [fileNodeId, importMap] of allImportMaps) {
+          const targetPaths = new Set(importMap.values());
+          for (const targetPath of targetPaths) {
+            const targetFileId = fileIdByPath.get(targetPath);
+            if (!targetFileId || targetFileId === fileNodeId) continue;
+            const edgeId = makeId(fileNodeId, targetFileId, 'imports_file');
+            try {
+              insertImport.run(edgeId, fileNodeId, targetFileId);
+              importsReconstructed++;
+            } catch { /* duplicate — already exists */ }
+          }
         }
-      }
+      });
+      insertAll();
     }
 
-    return { resolvedEdges, skippedDynamic, ambiguous };
+    return { resolvedEdges, skippedDynamic, ambiguous, reexportEdges, orphanImportsRemoved, importsReconstructed };
   },
 };