kirograph 1.0.0 → 1.2.1

package/dist/security/manifest/plugins/npm.js

@@ -28,6 +28,7 @@ var __toESM = (mod, isNodeMode, target) => (target = mod != null ? __create(__ge
 var __toCommonJS = (mod) => __copyProps(__defProp({}, "__esModule", { value: true }), mod);
 var npm_exports = {};
 __export(npm_exports, {
+  findNpmDuplicateVersions: () => findNpmDuplicateVersions,
   parseNpmManifest: () => parseNpmManifest
 });
 module.exports = __toCommonJS(npm_exports);
@@ -56,7 +57,7 @@ async function parseNpmManifest(manifestPath, projectRoot) {
     return [];
   }
   const resolvedVersions = loadResolvedVersions(manifestDir);
-  const license = extractNpmLicense(pkg);
+  const licenses = loadNpmLicenses(manifestDir);
   const dependencies = [];
   const warnings = [];
   for (const { field, scope } of SCOPE_FIELDS) {
@@ -79,6 +80,7 @@ async function parseNpmManifest(manifestPath, projectRoot) {
         continue;
       }
       const resolvedVersion = resolvedVersions.get(name);
+      const license = licenses.get(name);
       dependencies.push({
         name,
         declaredConstraint: constraint,
@@ -107,6 +109,7 @@ async function parseNpmManifest(manifestPath, projectRoot) {
       const alreadyDeclared = dependencies.some((d) => d.name === name);
       if (!alreadyDeclared) {
         const resolvedVersion = resolvedVersions.get(name);
+        const license = licenses.get(name);
         dependencies.push({
           name,
           declaredConstraint: constraint,
@@ -119,8 +122,94 @@ async function parseNpmManifest(manifestPath, projectRoot) {
       }
     }
   }
+  const directNames = new Set(dependencies.map((d) => d.name));
+  const lockRelativePath = relativeManifest.replace(/package\.json$/, "package-lock.json");
+  const npmLockPath = path.join(manifestDir, "package-lock.json");
+  if (fs.existsSync(npmLockPath)) {
+    dependencies.push(...extractTransitiveNpmDependencies(manifestDir, lockRelativePath, directNames));
+  } else {
+    for (const [name, version] of resolvedVersions) {
+      if (directNames.has(name)) continue;
+      dependencies.push({
+        name,
+        declaredConstraint: version,
+        resolvedVersion: version,
+        scope: "production",
+        ecosystem: "npm",
+        sourceManifest: relativeManifest
+      });
+    }
+  }
   return dependencies;
 }
+function findNpmDuplicateVersions(projectRoot) {
+  const versionsByName = /* @__PURE__ */ new Map();
+  const lockPath = path.join(projectRoot, "package-lock.json");
+  if (!fs.existsSync(lockPath)) return versionsByName;
+  let lockData;
+  try {
+    lockData = JSON.parse(fs.readFileSync(lockPath, "utf8"));
+  } catch {
+    return versionsByName;
+  }
+  if (typeof lockData !== "object" || lockData === null) return versionsByName;
+  const packages = lockData.packages;
+  if (typeof packages !== "object" || packages === null) return versionsByName;
+  for (const [key, value] of Object.entries(packages)) {
+    if (key === "") continue;
+    if (typeof value !== "object" || value === null) continue;
+    const pkg = value;
+    const version = pkg.version;
+    if (typeof version !== "string") continue;
+    const name = key.replace(/^.*node_modules\//, "");
+    if (!name) continue;
+    if (!versionsByName.has(name)) versionsByName.set(name, /* @__PURE__ */ new Set());
+    versionsByName.get(name).add(version);
+  }
+  for (const [name, versions] of versionsByName) {
+    if (versions.size <= 1) versionsByName.delete(name);
+  }
+  return versionsByName;
+}
+function extractTransitiveNpmDependencies(manifestDir, lockRelativePath, directNames) {
+  const lockPath = path.join(manifestDir, "package-lock.json");
+  if (!fs.existsSync(lockPath)) return [];
+  let lockData;
+  try {
+    lockData = JSON.parse(fs.readFileSync(lockPath, "utf8"));
+  } catch (err) {
+    (0, import_errors.logWarn)(`[sec:npm] Failed to parse ${lockRelativePath} for transitive dependencies: ${err instanceof Error ? err.message : String(err)}`);
+    return [];
+  }
+  if (typeof lockData !== "object" || lockData === null) return [];
+  const packages = lockData.packages;
+  if (typeof packages !== "object" || packages === null) return [];
+  const transitive = [];
+  const seen = /* @__PURE__ */ new Set();
+  for (const [key, value] of Object.entries(packages)) {
+    if (key === "") continue;
+    if (typeof value !== "object" || value === null) continue;
+    const pkg = value;
+    const name = key.replace(/^.*node_modules\//, "");
+    if (!name || directNames.has(name) || seen.has(name)) continue;
+    const version = pkg.version;
+    if (typeof version !== "string") continue;
+    seen.add(name);
+    const license = normalizeLicenseField(pkg);
+    transitive.push({
+      name,
+      // No real semver range exists at the project level for a transitive
+      // package — the resolved version is the only constraint we have.
+      declaredConstraint: version,
+      resolvedVersion: version,
+      scope: pkg.dev === true ? "development" : "production",
+      ecosystem: "npm",
+      sourceManifest: lockRelativePath,
+      ...license !== void 0 ? { license } : {}
+    });
+  }
+  return transitive;
+}
 function loadResolvedVersions(manifestDir) {
   const map = /* @__PURE__ */ new Map();
   const lockPath = path.join(manifestDir, "package-lock.json");
@@ -156,6 +245,31 @@ function loadResolvedVersions(manifestDir) {
   }
   return map;
 }
+function loadNpmLicenses(manifestDir) {
+  const map = /* @__PURE__ */ new Map();
+  const lockPath = path.join(manifestDir, "package-lock.json");
+  if (!fs.existsSync(lockPath)) return map;
+  let lockData;
+  try {
+    lockData = JSON.parse(fs.readFileSync(lockPath, "utf8"));
+  } catch (err) {
+    (0, import_errors.logWarn)(`[sec:npm] Failed to parse package-lock.json for license data: ${err instanceof Error ? err.message : String(err)}`);
+    return map;
+  }
+  if (typeof lockData !== "object" || lockData === null) return map;
+  const packages = lockData.packages;
+  if (typeof packages !== "object" || packages === null) return map;
+  for (const [key, value] of Object.entries(packages)) {
+    if (key === "") continue;
+    if (typeof value !== "object" || value === null) continue;
+    const pkg = value;
+    const name = key.replace(/^.*node_modules\//, "");
+    if (!name || map.has(name)) continue;
+    const license = normalizeLicenseField(pkg);
+    if (license !== void 0) map.set(name, license);
+  }
+  return map;
+}
 function extractFromPnpmLock(content, map) {
   for (const m of content.matchAll(/^[\s]*\/?(@?[a-zA-Z0-9._-]+(?:\/[a-zA-Z0-9._-]+)?)[@/]([0-9][a-zA-Z0-9._-]*)(?:\(.*?\))?:/gm)) {
     const name = m[1].replace(/^\//, "");
@@ -239,7 +353,7 @@ function extractPackageNameFromYarnHeader(header) {
   }
   return cleaned.slice(0, lastAtIndex);
 }
-function extractNpmLicense(pkg) {
+function normalizeLicenseField(pkg) {
   const raw = pkg["license"];
   if (typeof raw === "string" && raw.trim() !== "") {
     return raw.trim();
@@ -279,6 +393,7 @@ function isValidDependencyName(name) {
 }
 // Annotate the CommonJS export names for ESM import in node:
 0 && (module.exports = {
+  findNpmDuplicateVersions,
   parseNpmManifest
 });
 //# sourceMappingURL=npm.js.map

package/dist/security/manifest/plugins/npm.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../../src/security/manifest/plugins/npm.ts"],
-  "sourcesContent": ["/**\n * NPM Version Extraction Plugin for KiroGraph-Sec\n *\n * Extends the existing architecture npm parser to extract version constraints,\n * resolved versions (from lock files), and dependency scopes for security analysis.\n *\n * Reuses `npmParser` from `src/architecture/manifest/npm.ts` for discovery and\n * basic parsing, then layers on version/scope extraction.\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport type { ParsedDependency } from '../../types';\nimport { logWarn } from '../../../errors';\n\n/** Scope fields in package.json mapped to their ParsedDependency scope */\nconst SCOPE_FIELDS: Array<{ field: string; scope: ParsedDependency['scope'] }> = [\n  { field: 'dependencies', scope: 'production' },\n  { field: 'devDependencies', scope: 'development' },\n  { field: 'optionalDependencies', scope: 'optional' },\n];\n\n/**\n * Resolved version map: package name \u2192 resolved version string.\n * Built from package-lock.json or yarn.lock.\n */\ntype ResolvedVersionMap = Map<string, string>;\n\n/**\n * Parse an npm package.json manifest and extract dependency declarations\n * with version constraints, scopes, and resolved versions from lock files.\n *\n * @param manifestPath - Absolute path to the package.json file\n * @param projectRoot - Absolute path to the project root directory\n * @returns Array of parsed dependencies with version and scope information\n */\nexport async function parseNpmManifest(\n  manifestPath: string,\n  projectRoot: string,\n): Promise<ParsedDependency[]> {\n  const manifestDir = path.dirname(manifestPath);\n  const relativeManifest = path.relative(projectRoot, manifestPath).replace(/\\\\/g, '/');\n\n  // Read and parse the package.json\n  let pkg: Record<string, unknown>;\n  try {\n    const raw = fs.readFileSync(manifestPath, 'utf8');\n    const parsed = JSON.parse(raw);\n    if (typeof parsed !== 'object' || parsed === null || Array.isArray(parsed)) {\n      logWarn(`[sec:npm] Invalid package.json structure at ${relativeManifest}`);\n      return [];\n    }\n    pkg = parsed as Record<string, unknown>;\n  } catch (err) {\n    logWarn(`[sec:npm] Failed to read/parse ${relativeManifest}: ${err instanceof Error ? err.message : String(err)}`);\n    return [];\n  }\n\n  // Attempt to load resolved versions from lock file\n  const resolvedVersions = loadResolvedVersions(manifestDir);\n\n  // Extract the package-level license\n  const license = extractNpmLicense(pkg);\n\n  // Extract dependencies from each scope field\n  const dependencies: ParsedDependency[] = [];\n  const warnings: Array<{ name: string; reason: string }> = [];\n\n  for (const { field, scope } of SCOPE_FIELDS) {\n    const depsObj = pkg[field];\n    if (depsObj === undefined || depsObj === null) continue;\n\n    if (typeof depsObj !== 'object' || Array.isArray(depsObj)) {\n      logWarn(`[sec:npm] Invalid \"${field}\" field in ${relativeManifest} \u2014 expected object, got ${typeof depsObj}`);\n      continue;\n    }\n\n    const entries = Object.entries(depsObj as Record<string, unknown>);\n    for (const [name, constraint] of entries) {\n      // Validate the dependency entry\n      if (!isValidDependencyName(name)) {\n        logWarn(`[sec:npm] Invalid dependency name \"${name}\" in ${relativeManifest} (${field}) \u2014 skipping`);\n        warnings.push({ name, reason: 'invalid name' });\n        continue;\n      }\n\n      if (typeof constraint !== 'string' || constraint.trim() === '') {\n        logWarn(`[sec:npm] Invalid version constraint for \"${name}\" in ${relativeManifest} (${field}) \u2014 skipping`);\n        warnings.push({ name, reason: 'invalid constraint' });\n        continue;\n      }\n\n      const resolvedVersion = resolvedVersions.get(name);\n\n      dependencies.push({\n        name,\n        declaredConstraint: constraint,\n        resolvedVersion,\n        scope,\n        ecosystem: 'npm',\n        sourceManifest: relativeManifest,\n        ...(license !== undefined ? { license } : {}),\n      });\n    }\n  }\n\n  // Also handle peerDependencies \u2014 default to production scope\n  const peerDeps = pkg.peerDependencies;\n  if (peerDeps && typeof peerDeps === 'object' && !Array.isArray(peerDeps)) {\n    const peerEntries = Object.entries(peerDeps as Record<string, unknown>);\n    for (const [name, constraint] of peerEntries) {\n      if (!isValidDependencyName(name)) {\n        logWarn(`[sec:npm] Invalid peer dependency name \"${name}\" in ${relativeManifest} \u2014 skipping`);\n        warnings.push({ name, reason: 'invalid name' });\n        continue;\n      }\n\n      if (typeof constraint !== 'string' || constraint.trim() === '') {\n        logWarn(`[sec:npm] Invalid version constraint for peer dependency \"${name}\" in ${relativeManifest} \u2014 skipping`);\n        warnings.push({ name, reason: 'invalid constraint' });\n        continue;\n      }\n\n      // Only add if not already declared in another scope\n      const alreadyDeclared = dependencies.some(d => d.name === name);\n      if (!alreadyDeclared) {\n        const resolvedVersion = resolvedVersions.get(name);\n        dependencies.push({\n          name,\n          declaredConstraint: constraint,\n          resolvedVersion,\n          scope: 'production',\n          ecosystem: 'npm',\n          sourceManifest: relativeManifest,\n          ...(license !== undefined ? { license } : {}),\n        });\n      }\n    }\n  }\n\n  return dependencies;\n}\n\n/**\n * Attempt to load resolved versions from package-lock.json, pnpm-lock.yaml,\n * or yarn.lock in the given directory. Returns an empty map if none is available.\n */\nfunction loadResolvedVersions(manifestDir: string): ResolvedVersionMap {\n  const map: ResolvedVersionMap = new Map();\n\n  // Try package-lock.json first (preferred \u2014 npm)\n  const lockPath = path.join(manifestDir, 'package-lock.json');\n  if (fs.existsSync(lockPath)) {\n    try {\n      const lockContent = fs.readFileSync(lockPath, 'utf8');\n      const lockData = JSON.parse(lockContent);\n      extractFromPackageLock(lockData, map);\n      return map;\n    } catch (err) {\n      logWarn(`[sec:npm] Failed to parse package-lock.json: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  // Try pnpm-lock.yaml (pnpm)\n  const pnpmLockPath = path.join(manifestDir, 'pnpm-lock.yaml');\n  if (fs.existsSync(pnpmLockPath)) {\n    try {\n      const pnpmContent = fs.readFileSync(pnpmLockPath, 'utf8');\n      extractFromPnpmLock(pnpmContent, map);\n      return map;\n    } catch (err) {\n      logWarn(`[sec:npm] Failed to parse pnpm-lock.yaml: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  // Fall back to yarn.lock\n  const yarnLockPath = path.join(manifestDir, 'yarn.lock');\n  if (fs.existsSync(yarnLockPath)) {\n    try {\n      const yarnContent = fs.readFileSync(yarnLockPath, 'utf8');\n      extractFromYarnLock(yarnContent, map);\n      return map;\n    } catch (err) {\n      logWarn(`[sec:npm] Failed to parse yarn.lock: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  return map;\n}\n\n/**\n * Extract resolved versions from pnpm-lock.yaml (v5, v6, v9 formats).\n *\n * v5/v6: packages section with keys like \"/express/4.18.2\" or \"/express@4.18.2\"\n * v9:    snapshots section with keys like \"express@4.18.2\" and\n *        packages section with \"express@4.18.2: {version: ...}\" (optional)\n */\nfunction extractFromPnpmLock(content: string, map: ResolvedVersionMap): void {\n  // v9 format: package entries under `packages:` or `snapshots:`\n  // Key format: \"name@version\" or \"@scope/name@version\"\n  // We extract name@version pairs from both sections.\n\n  // Match lines like:  /express/4.18.2:  or  /express@4.18.2:  or  express@4.18.2:\n  for (const m of content.matchAll(/^[\\s]*\\/?(@?[a-zA-Z0-9._-]+(?:\\/[a-zA-Z0-9._-]+)?)[@/]([0-9][a-zA-Z0-9._-]*)(?:\\(.*?\\))?:/gm)) {\n    const name = m[1].replace(/^\\//, ''); // strip leading slash for scoped packages\n    const version = m[2];\n    if (name && version && !map.has(name)) {\n      map.set(name, version);\n    }\n  }\n}\n\n/**\n * Extract resolved versions from package-lock.json (supports v2 and v3 format).\n */\nfunction extractFromPackageLock(lockData: unknown, map: ResolvedVersionMap): void {\n  if (typeof lockData !== 'object' || lockData === null) return;\n  const lock = lockData as Record<string, unknown>;\n\n  // lockfileVersion 2/3: uses \"packages\" field with \"\" as root\n  const packages = lock.packages;\n  if (typeof packages === 'object' && packages !== null) {\n    for (const [key, value] of Object.entries(packages as Record<string, unknown>)) {\n      if (key === '') continue; // skip root\n      if (typeof value !== 'object' || value === null) continue;\n      const pkg = value as Record<string, unknown>;\n      const version = pkg.version;\n      if (typeof version !== 'string') continue;\n\n      // Key format: \"node_modules/<name>\" or \"node_modules/@scope/name\"\n      const name = key.replace(/^.*node_modules\\//, '');\n      if (name && !map.has(name)) {\n        map.set(name, version);\n      }\n    }\n    return;\n  }\n\n  // lockfileVersion 1: uses \"dependencies\" field\n  const dependencies = lock.dependencies;\n  if (typeof dependencies === 'object' && dependencies !== null) {\n    extractFromLockV1Dependencies(dependencies as Record<string, unknown>, map);\n  }\n}\n\n/**\n * Recursively extract versions from lockfileVersion 1 dependencies.\n */\nfunction extractFromLockV1Dependencies(\n  deps: Record<string, unknown>,\n  map: ResolvedVersionMap,\n): void {\n  for (const [name, value] of Object.entries(deps)) {\n    if (typeof value !== 'object' || value === null) continue;\n    const dep = value as Record<string, unknown>;\n    const version = dep.version;\n    if (typeof version === 'string' && !map.has(name)) {\n      map.set(name, version);\n    }\n    // Recurse into nested dependencies\n    const nested = dep.dependencies;\n    if (typeof nested === 'object' && nested !== null) {\n      extractFromLockV1Dependencies(nested as Record<string, unknown>, map);\n    }\n  }\n}\n\n/**\n * Extract resolved versions from yarn.lock (v1 format).\n * yarn.lock uses a custom format, not JSON.\n */\nfunction extractFromYarnLock(content: string, map: ResolvedVersionMap): void {\n  const lines = content.split('\\n');\n  let currentPackageName: string | null = null;\n\n  for (const line of lines) {\n    // Skip comments and empty lines\n    if (line.startsWith('#') || line.trim() === '') {\n      currentPackageName = null;\n      continue;\n    }\n\n    // Package header line: \"package-name@version-range:\" or \"@scope/name@range:\"\n    // Can also be: \"package-name@range1, package-name@range2:\"\n    if (!line.startsWith(' ') && line.endsWith(':')) {\n      const header = line.slice(0, -1); // remove trailing ':'\n      // Extract package name from the first entry (before @version)\n      const name = extractPackageNameFromYarnHeader(header);\n      currentPackageName = name;\n      continue;\n    }\n\n    // Version line: \"  version \"x.y.z\"\"\n    if (currentPackageName && line.trim().startsWith('version ')) {\n      const versionMatch = line.match(/version\\s+\"([^\"]+)\"/);\n      if (versionMatch && !map.has(currentPackageName)) {\n        map.set(currentPackageName, versionMatch[1]);\n      }\n      currentPackageName = null;\n    }\n  }\n}\n\n/**\n * Extract the package name from a yarn.lock header line.\n * Handles formats like:\n *   - \"express@^4.17.1\"\n *   - \"@types/node@^18.0.0\"\n *   - \"express@^4.17.1, express@^4.18.0\"\n *   - '\"express@^4.17.1\"'\n */\nfunction extractPackageNameFromYarnHeader(header: string): string | null {\n  // Take the first entry if comma-separated\n  const firstEntry = header.split(',')[0].trim();\n  // Remove surrounding quotes if present\n  const cleaned = firstEntry.replace(/^[\"']|[\"']$/g, '');\n\n  // Find the last @ that separates name from version\n  // For scoped packages (@scope/name@version), we need the last @\n  const lastAtIndex = cleaned.lastIndexOf('@');\n  if (lastAtIndex <= 0) return null; // no @ or starts with @ (scoped without version)\n\n  // For scoped packages, check if the first char is @\n  if (cleaned.startsWith('@')) {\n    // @scope/name@version \u2014 find the @ after the scope\n    const afterScope = cleaned.indexOf('/', 1);\n    if (afterScope === -1) return null;\n    const atAfterName = cleaned.indexOf('@', afterScope);\n    if (atAfterName === -1) return cleaned; // no version part\n    return cleaned.slice(0, atAfterName);\n  }\n\n  return cleaned.slice(0, lastAtIndex);\n}\n\n/**\n * Extract the license field from a parsed package.json object.\n * Handles both string format (`\"MIT\"`) and object format (`{\"type\":\"MIT\"}`).\n */\nfunction extractNpmLicense(pkg: Record<string, unknown>): string | undefined {\n  const raw = pkg['license'];\n  if (typeof raw === 'string' && raw.trim() !== '') {\n    return raw.trim();\n  }\n  if (typeof raw === 'object' && raw !== null && !Array.isArray(raw)) {\n    const licObj = raw as Record<string, unknown>;\n    if (typeof licObj['type'] === 'string' && licObj['type'].trim() !== '') {\n      return licObj['type'].trim();\n    }\n  }\n  // Handle legacy \"licenses\" array\n  const licenses = pkg['licenses'];\n  if (Array.isArray(licenses) && licenses.length > 0) {\n    const first = licenses[0];\n    if (typeof first === 'object' && first !== null) {\n      const lic = first as Record<string, unknown>;\n      if (typeof lic['type'] === 'string' && lic['type'].trim() !== '') {\n        return lic['type'].trim();\n      }\n    }\n    if (typeof first === 'string' && first.trim() !== '') {\n      return first.trim();\n    }\n  }\n  return undefined;\n}\n\n/**\n * Validate that a dependency name follows npm naming conventions.\n * Must be non-empty, not start with a dot or underscore (unless scoped),\n * and contain only valid characters.\n */\nfunction isValidDependencyName(name: string): boolean {\n  if (!name || typeof name !== 'string') return false;\n  if (name.length > 214) return false;\n\n  // Scoped packages: @scope/name\n  if (name.startsWith('@')) {\n    const parts = name.split('/');\n    if (parts.length !== 2) return false;\n    if (!parts[0] || !parts[1]) return false;\n    return true;\n  }\n\n  // Unscoped: must not start with . or _\n  if (name.startsWith('.') || name.startsWith('_')) return false;\n\n  return true;\n}\n"],
-  "mappings": 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Add them here.\n  const directNames = new Set(dependencies.map(d => d.name));\n  const lockRelativePath = relativeManifest.replace(/package\\.json$/, 'package-lock.json');\n  const npmLockPath = path.join(manifestDir, 'package-lock.json');\n  if (fs.existsSync(npmLockPath)) {\n    // package-lock.json (v2/v3) carries a per-package \"dev\" flag \u2014 parse it\n    // directly so transitive dev-only dependencies keep the right scope.\n    dependencies.push(...extractTransitiveNpmDependencies(manifestDir, lockRelativePath, directNames));\n  } else {\n    // pnpm-lock.yaml, yarn.lock, or a lockfileVersion 1 package-lock.json:\n    // resolvedVersions already has every package the lock file resolved,\n    // direct or transitive \u2014 it just doesn't carry a dev/prod distinction,\n    // so default newly-added transitive entries to 'production'.\n    for (const [name, version] of resolvedVersions) {\n      if (directNames.has(name)) continue;\n      dependencies.push({\n        name,\n        declaredConstraint: version,\n        resolvedVersion: version,\n        scope: 'production',\n        ecosystem: 'npm',\n        sourceManifest: relativeManifest,\n      });\n    }\n  }\n\n  return dependencies;\n}\n\n/**\n * Find every npm package name that resolves to more than one distinct\n * version somewhere in package-lock.json's dependency tree. npm's nested\n * node_modules layout can install different versions of the same package\n * at different paths (e.g. a top-level `qs@6.16.0` alongside a\n * `body-parser`-nested `qs@6.15.3`) \u2014 but a Dependency_Node only records one\n * `resolved_version`. Used by vulnerability enrichment to also check every\n * other installed copy, not just whichever version ended up recorded.\n *\n * Only the top-level package-lock.json (lockfile v2/v3 \"packages\" map) is\n * checked \u2014 a monorepo with per-package lock files, or pnpm/yarn projects,\n * won't get this extra check (they still get the single recorded version).\n *\n * Returns a map from package name to the full set of distinct versions\n * found; names with only one version are omitted.\n */\nexport function findNpmDuplicateVersions(projectRoot: string): Map<string, Set<string>> {\n  const versionsByName = new Map<string, Set<string>>();\n\n  const lockPath = path.join(projectRoot, 'package-lock.json');\n  if (!fs.existsSync(lockPath)) return versionsByName;\n\n  let lockData: unknown;\n  try {\n    lockData = JSON.parse(fs.readFileSync(lockPath, 'utf8'));\n  } catch {\n    return versionsByName;\n  }\n\n  if (typeof lockData !== 'object' || lockData === null) return versionsByName;\n  const packages = (lockData as Record<string, unknown>).packages;\n  if (typeof packages !== 'object' || packages === null) return versionsByName;\n\n  for (const [key, value] of Object.entries(packages as Record<string, unknown>)) {\n    if (key === '') continue; // skip the root project entry\n    if (typeof value !== 'object' || value === null) continue;\n    const pkg = value as Record<string, unknown>;\n\n    const version = pkg.version;\n    if (typeof version !== 'string') continue;\n\n    const name = key.replace(/^.*node_modules\\//, '');\n    if (!name) continue;\n\n    if (!versionsByName.has(name)) versionsByName.set(name, new Set());\n    versionsByName.get(name)!.add(version);\n  }\n\n  for (const [name, versions] of versionsByName) {\n    if (versions.size <= 1) versionsByName.delete(name);\n  }\n\n  return versionsByName;\n}\n\n/**\n * Extract every package listed in package-lock.json's \"packages\" map (lockfile\n * v2/v3) that isn't already a direct dependency. These are transitive-only\n * packages \u2014 e.g. a sub-dependency three levels deep \u2014 that `npm audit` reports\n * on but that package.json never mentions.\n */\nfunction extractTransitiveNpmDependencies(\n  manifestDir: string,\n  lockRelativePath: string,\n  directNames: Set<string>,\n): ParsedDependency[] {\n  const lockPath = path.join(manifestDir, 'package-lock.json');\n  if (!fs.existsSync(lockPath)) return [];\n\n  let lockData: unknown;\n  try {\n    lockData = JSON.parse(fs.readFileSync(lockPath, 'utf8'));\n  } catch (err) {\n    logWarn(`[sec:npm] Failed to parse ${lockRelativePath} for transitive dependencies: ${err instanceof Error ? err.message : String(err)}`);\n    return [];\n  }\n\n  if (typeof lockData !== 'object' || lockData === null) return [];\n  const packages = (lockData as Record<string, unknown>).packages;\n  if (typeof packages !== 'object' || packages === null) return [];\n\n  const transitive: ParsedDependency[] = [];\n  const seen = new Set<string>();\n\n  for (const [key, value] of Object.entries(packages as Record<string, unknown>)) {\n    if (key === '') continue; // skip the root project entry\n    if (typeof value !== 'object' || value === null) continue;\n    const pkg = value as Record<string, unknown>;\n\n    const name = key.replace(/^.*node_modules\\//, '');\n    if (!name || directNames.has(name) || seen.has(name)) continue;\n\n    const version = pkg.version;\n    if (typeof version !== 'string') continue;\n\n    seen.add(name);\n    const license = normalizeLicenseField(pkg);\n    transitive.push({\n      name,\n      // No real semver range exists at the project level for a transitive\n      // package \u2014 the resolved version is the only constraint we have.\n      declaredConstraint: version,\n      resolvedVersion: version,\n      scope: pkg.dev === true ? 'development' : 'production',\n      ecosystem: 'npm',\n      sourceManifest: lockRelativePath,\n      ...(license !== undefined ? { license } : {}),\n    });\n  }\n\n  return transitive;\n}\n\n/**\n * Attempt to load resolved versions from package-lock.json, pnpm-lock.yaml,\n * or yarn.lock in the given directory. Returns an empty map if none is available.\n */\nfunction loadResolvedVersions(manifestDir: string): ResolvedVersionMap {\n  const map: ResolvedVersionMap = new Map();\n\n  // Try package-lock.json first (preferred \u2014 npm)\n  const lockPath = path.join(manifestDir, 'package-lock.json');\n  if (fs.existsSync(lockPath)) {\n    try {\n      const lockContent = fs.readFileSync(lockPath, 'utf8');\n      const lockData = JSON.parse(lockContent);\n      extractFromPackageLock(lockData, map);\n      return map;\n    } catch (err) {\n      logWarn(`[sec:npm] Failed to parse package-lock.json: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  // Try pnpm-lock.yaml (pnpm)\n  const pnpmLockPath = path.join(manifestDir, 'pnpm-lock.yaml');\n  if (fs.existsSync(pnpmLockPath)) {\n    try {\n      const pnpmContent = fs.readFileSync(pnpmLockPath, 'utf8');\n      extractFromPnpmLock(pnpmContent, map);\n      return map;\n    } catch (err) {\n      logWarn(`[sec:npm] Failed to parse pnpm-lock.yaml: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  // Fall back to yarn.lock\n  const yarnLockPath = path.join(manifestDir, 'yarn.lock');\n  if (fs.existsSync(yarnLockPath)) {\n    try {\n      const yarnContent = fs.readFileSync(yarnLockPath, 'utf8');\n      extractFromYarnLock(yarnContent, map);\n      return map;\n    } catch (err) {\n      logWarn(`[sec:npm] Failed to parse yarn.lock: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  return map;\n}\n\n/**\n * Load each installed package's own SPDX license from package-lock.json's\n * \"packages\" map (npm v7+ lockfile v2/v3). npm records the \"license\" field\n * from each package's own package.json there when it exists \u2014 this is the\n * dependency's *own* license, not the consuming project's, so it's the\n * correct source for license-compliance checks (issue #39 follow-up: the\n * project's own root package.json \"license\" field was previously applied to\n * every dependency, which is both wrong when present and leaves every\n * transitive-only package \u2014 the majority in most trees \u2014 as \"unknown\").\n *\n * pnpm-lock.yaml and yarn.lock don't carry a comparably structured per-package\n * license field, so this only covers package-lock.json for now; other lock\n * formats fall back to no license data, same as before this fix.\n */\nfunction loadNpmLicenses(manifestDir: string): LicenseMap {\n  const map: LicenseMap = new Map();\n\n  const lockPath = path.join(manifestDir, 'package-lock.json');\n  if (!fs.existsSync(lockPath)) return map;\n\n  let lockData: unknown;\n  try {\n    lockData = JSON.parse(fs.readFileSync(lockPath, 'utf8'));\n  } catch (err) {\n    logWarn(`[sec:npm] Failed to parse package-lock.json for license data: ${err instanceof Error ? err.message : String(err)}`);\n    return map;\n  }\n\n  if (typeof lockData !== 'object' || lockData === null) return map;\n  const packages = (lockData as Record<string, unknown>).packages;\n  if (typeof packages !== 'object' || packages === null) return map;\n\n  for (const [key, value] of Object.entries(packages as Record<string, unknown>)) {\n    if (key === '') continue; // skip the root project entry\n    if (typeof value !== 'object' || value === null) continue;\n    const pkg = value as Record<string, unknown>;\n\n    const name = key.replace(/^.*node_modules\\//, '');\n    if (!name || map.has(name)) continue;\n\n    const license = normalizeLicenseField(pkg);\n    if (license !== undefined) map.set(name, license);\n  }\n\n  return map;\n}\n\n/**\n * Extract resolved versions from pnpm-lock.yaml (v5, v6, v9 formats).\n *\n * v5/v6: packages section with keys like \"/express/4.18.2\" or \"/express@4.18.2\"\n * v9:    snapshots section with keys like \"express@4.18.2\" and\n *        packages section with \"express@4.18.2: {version: ...}\" (optional)\n */\nfunction extractFromPnpmLock(content: string, map: ResolvedVersionMap): void {\n  // v9 format: package entries under `packages:` or `snapshots:`\n  // Key format: \"name@version\" or \"@scope/name@version\"\n  // We extract name@version pairs from both sections.\n\n  // Match lines like:  /express/4.18.2:  or  /express@4.18.2:  or  express@4.18.2:\n  for (const m of content.matchAll(/^[\\s]*\\/?(@?[a-zA-Z0-9._-]+(?:\\/[a-zA-Z0-9._-]+)?)[@/]([0-9][a-zA-Z0-9._-]*)(?:\\(.*?\\))?:/gm)) {\n    const name = m[1].replace(/^\\//, ''); // strip leading slash for scoped packages\n    const version = m[2];\n    if (name && version && !map.has(name)) {\n      map.set(name, version);\n    }\n  }\n}\n\n/**\n * Extract resolved versions from package-lock.json (supports v2 and v3 format).\n */\nfunction extractFromPackageLock(lockData: unknown, map: ResolvedVersionMap): void {\n  if (typeof lockData !== 'object' || lockData === null) return;\n  const lock = lockData as Record<string, unknown>;\n\n  // lockfileVersion 2/3: uses \"packages\" field with \"\" as root\n  const packages = lock.packages;\n  if (typeof packages === 'object' && packages !== null) {\n    for (const [key, value] of Object.entries(packages as Record<string, unknown>)) {\n      if (key === '') continue; // skip root\n      if (typeof value !== 'object' || value === null) continue;\n      const pkg = value as Record<string, unknown>;\n      const version = pkg.version;\n      if (typeof version !== 'string') continue;\n\n      // Key format: \"node_modules/<name>\" or \"node_modules/@scope/name\"\n      const name = key.replace(/^.*node_modules\\//, '');\n      if (name && !map.has(name)) {\n        map.set(name, version);\n      }\n    }\n    return;\n  }\n\n  // lockfileVersion 1: uses \"dependencies\" field\n  const dependencies = lock.dependencies;\n  if (typeof dependencies === 'object' && dependencies !== null) {\n    extractFromLockV1Dependencies(dependencies as Record<string, unknown>, map);\n  }\n}\n\n/**\n * Recursively extract versions from lockfileVersion 1 dependencies.\n */\nfunction extractFromLockV1Dependencies(\n  deps: Record<string, unknown>,\n  map: ResolvedVersionMap,\n): void {\n  for (const [name, value] of Object.entries(deps)) {\n    if (typeof value !== 'object' || value === null) continue;\n    const dep = value as Record<string, unknown>;\n    const version = dep.version;\n    if (typeof version === 'string' && !map.has(name)) {\n      map.set(name, version);\n    }\n    // Recurse into nested dependencies\n    const nested = dep.dependencies;\n    if (typeof nested === 'object' && nested !== null) {\n      extractFromLockV1Dependencies(nested as Record<string, unknown>, map);\n    }\n  }\n}\n\n/**\n * Extract resolved versions from yarn.lock (v1 format).\n * yarn.lock uses a custom format, not JSON.\n */\nfunction extractFromYarnLock(content: string, map: ResolvedVersionMap): void {\n  const lines = content.split('\\n');\n  let currentPackageName: string | null = null;\n\n  for (const line of lines) {\n    // Skip comments and empty lines\n    if (line.startsWith('#') || line.trim() === '') {\n      currentPackageName = null;\n      continue;\n    }\n\n    // Package header line: \"package-name@version-range:\" or \"@scope/name@range:\"\n    // Can also be: \"package-name@range1, package-name@range2:\"\n    if (!line.startsWith(' ') && line.endsWith(':')) {\n      const header = line.slice(0, -1); // remove trailing ':'\n      // Extract package name from the first entry (before @version)\n      const name = extractPackageNameFromYarnHeader(header);\n      currentPackageName = name;\n      continue;\n    }\n\n    // Version line: \"  version \"x.y.z\"\"\n    if (currentPackageName && line.trim().startsWith('version ')) {\n      const versionMatch = line.match(/version\\s+\"([^\"]+)\"/);\n      if (versionMatch && !map.has(currentPackageName)) {\n        map.set(currentPackageName, versionMatch[1]);\n      }\n      currentPackageName = null;\n    }\n  }\n}\n\n/**\n * Extract the package name from a yarn.lock header line.\n * Handles formats like:\n *   - \"express@^4.17.1\"\n *   - \"@types/node@^18.0.0\"\n *   - \"express@^4.17.1, express@^4.18.0\"\n *   - '\"express@^4.17.1\"'\n */\nfunction extractPackageNameFromYarnHeader(header: string): string | null {\n  // Take the first entry if comma-separated\n  const firstEntry = header.split(',')[0].trim();\n  // Remove surrounding quotes if present\n  const cleaned = firstEntry.replace(/^[\"']|[\"']$/g, '');\n\n  // Find the last @ that separates name from version\n  // For scoped packages (@scope/name@version), we need the last @\n  const lastAtIndex = cleaned.lastIndexOf('@');\n  if (lastAtIndex <= 0) return null; // no @ or starts with @ (scoped without version)\n\n  // For scoped packages, check if the first char is @\n  if (cleaned.startsWith('@')) {\n    // @scope/name@version \u2014 find the @ after the scope\n    const afterScope = cleaned.indexOf('/', 1);\n    if (afterScope === -1) return null;\n    const atAfterName = cleaned.indexOf('@', afterScope);\n    if (atAfterName === -1) return cleaned; // no version part\n    return cleaned.slice(0, atAfterName);\n  }\n\n  return cleaned.slice(0, lastAtIndex);\n}\n\n/**\n * Normalize a package's `license`/`licenses` field into a single SPDX-ish\n * string. Handles the string format (`\"MIT\"`), the object format\n * (`{\"type\":\"MIT\"}`), and the legacy `licenses` array format. Used both for\n * package-lock.json's per-package `license` entries and, if ever needed,\n * a raw package.json object.\n */\nfunction normalizeLicenseField(pkg: Record<string, unknown>): string | undefined {\n  const raw = pkg['license'];\n  if (typeof raw === 'string' && raw.trim() !== '') {\n    return raw.trim();\n  }\n  if (typeof raw === 'object' && raw !== null && !Array.isArray(raw)) {\n    const licObj = raw as Record<string, unknown>;\n    if (typeof licObj['type'] === 'string' && licObj['type'].trim() !== '') {\n      return licObj['type'].trim();\n    }\n  }\n  // Handle legacy \"licenses\" array\n  const licenses = pkg['licenses'];\n  if (Array.isArray(licenses) && licenses.length > 0) {\n    const first = licenses[0];\n    if (typeof first === 'object' && first !== null) {\n      const lic = first as Record<string, unknown>;\n      if (typeof lic['type'] === 'string' && lic['type'].trim() !== '') {\n        return lic['type'].trim();\n      }\n    }\n    if (typeof first === 'string' && first.trim() !== '') {\n      return first.trim();\n    }\n  }\n  return undefined;\n}\n\n/**\n * Validate that a dependency name follows npm naming conventions.\n * Must be non-empty, not start with a dot or underscore (unless scoped),\n * and contain only valid characters.\n */\nfunction isValidDependencyName(name: string): boolean {\n  if (!name || typeof name !== 'string') return false;\n  if (name.length > 214) return false;\n\n  // Scoped packages: @scope/name\n  if (name.startsWith('@')) {\n    const parts = name.split('/');\n    if (parts.length !== 2) return false;\n    if (!parts[0] || !parts[1]) return false;\n    return true;\n  }\n\n  // Unscoped: must not start with . or _\n  if (name.startsWith('.') || name.startsWith('_')) return false;\n\n  return true;\n}\n"],
+  "mappings": 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   "names": []
 }

package/dist/security/manifest/plugins/nuget.js

@@ -82,6 +82,19 @@ async function parseNugetManifest(manifestPath, projectRoot) {
       (0, import_errors.logWarn)(`[sec:nuget] Failed to read ${relativePackagesConfig}: ${err instanceof Error ? err.message : String(err)}`);
     }
   }
+  const directNames = new Set(dependencies.map((d) => d.name.toLowerCase()));
+  const lockRelativePath = path.relative(projectRoot, path.join(manifestDir, "packages.lock.json")).replace(/\\/g, "/");
+  for (const [name, version] of resolvedVersions) {
+    if (directNames.has(name)) continue;
+    dependencies.push({
+      name,
+      declaredConstraint: version,
+      resolvedVersion: version,
+      scope: "production",
+      ecosystem: "nuget",
+      sourceManifest: lockRelativePath
+    });
+  }
   return dependencies;
 }
 function extractPackageReferences(content, relativeManifest) {

package/dist/security/manifest/plugins/nuget.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../../src/security/manifest/plugins/nuget.ts"],
-  "sourcesContent": ["/**\n * NuGet Version Extraction Plugin for KiroGraph-Sec\n *\n * Extends the existing architecture csproj parser to extract version constraints,\n * resolved versions (from packages.lock.json), and dependency scopes for security analysis.\n *\n * Reuses `csprojParser` from `src/architecture/manifest/csproj.ts` for discovery and\n * basic parsing, then layers on version/scope extraction.\n *\n * Handles:\n * - Inline attribute format: `<PackageReference Include=\"Name\" Version=\"1.0.0\"/>`\n * - Multi-line child element format: `<PackageReference Include=\"Name\"><Version>1.0.0</Version></PackageReference>`\n * - Legacy packages.config: `<package id=\"Name\" version=\"1.0.0\" targetFramework=\"...\"/>`\n * - Lock file packages.lock.json for resolved versions\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport type { ParsedDependency } from '../../types';\nimport { logWarn } from '../../../errors';\n\n/**\n * Resolved version map: package name (lower-cased) \u2192 resolved version string.\n * Built from packages.lock.json.\n */\ntype ResolvedVersionMap = Map<string, string>;\n\n/**\n * Parse a .csproj manifest and extract NuGet dependency declarations\n * with version constraints, scopes, and resolved versions from packages.lock.json.\n * Also parses a packages.config in the same directory if present.\n *\n * @param manifestPath - Absolute path to the .csproj file\n * @param projectRoot - Absolute path to the project root directory\n * @returns Array of parsed dependencies with version and scope information\n */\nexport async function parseNugetManifest(\n  manifestPath: string,\n  projectRoot: string,\n): Promise<ParsedDependency[]> {\n  const manifestDir = path.dirname(manifestPath);\n  const relativeManifest = path.relative(projectRoot, manifestPath).replace(/\\\\/g, '/');\n\n  // Read the .csproj content\n  let content: string;\n  try {\n    content = fs.readFileSync(manifestPath, 'utf8');\n  } catch (err) {\n    logWarn(`[sec:nuget] Failed to read ${relativeManifest}: ${err instanceof Error ? err.message : String(err)}`);\n    return [];\n  }\n\n  // Attempt to load resolved versions from packages.lock.json\n  const resolvedVersions = loadResolvedVersions(manifestDir);\n\n  // Extract project-level license from .csproj\n  const license = extractNugetLicense(content);\n\n  const dependencies: ParsedDependency[] = [];\n\n  // Extract from .csproj PackageReference elements\n  const csprojDeps = extractPackageReferences(content, relativeManifest);\n  for (const dep of csprojDeps) {\n    const resolvedVersion = resolvedVersions.get(dep.name.toLowerCase());\n    dependencies.push({\n      name: dep.name,\n      declaredConstraint: dep.constraint,\n      resolvedVersion,\n      scope: dep.scope,\n      ecosystem: 'nuget',\n      sourceManifest: relativeManifest,\n      ...(license !== undefined ? { license } : {}),\n    });\n  }\n\n  // Also parse packages.config in the same directory (legacy NuGet)\n  const packagesConfigPath = path.join(manifestDir, 'packages.config');\n  if (fs.existsSync(packagesConfigPath)) {\n    const relativePackagesConfig = path.relative(projectRoot, packagesConfigPath).replace(/\\\\/g, '/');\n    try {\n      const packagesConfigContent = fs.readFileSync(packagesConfigPath, 'utf8');\n      const legacyDeps = extractPackagesConfig(packagesConfigContent, relativePackagesConfig);\n      for (const dep of legacyDeps) {\n        const resolvedVersion = resolvedVersions.get(dep.name.toLowerCase());\n        dependencies.push({\n          name: dep.name,\n          declaredConstraint: dep.constraint,\n          resolvedVersion,\n          scope: dep.scope,\n          ecosystem: 'nuget',\n          sourceManifest: relativePackagesConfig,\n          ...(license !== undefined ? { license } : {}),\n        });\n      }\n    } catch (err) {\n      logWarn(`[sec:nuget] Failed to read ${relativePackagesConfig}: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  return dependencies;\n}\n\n/**\n * A raw dependency entry extracted from a .csproj or packages.config file.\n */\ninterface RawDependency {\n  name: string;\n  constraint: string;\n  scope: ParsedDependency['scope'];\n}\n\n/**\n * Extract PackageReference entries from .csproj XML content.\n *\n * Handles:\n * - Inline: `<PackageReference Include=\"Newtonsoft.Json\" Version=\"13.0.1\" />`\n * - With PrivateAssets=\"all\": `<PackageReference Include=\"MSTest.TestFramework\" Version=\"3.1.1\" PrivateAssets=\"all\" />`\n * - Multi-line child: `<PackageReference Include=\"Name\"><Version>1.0.0</Version></PackageReference>`\n */\nfunction extractPackageReferences(content: string, relativeManifest: string): RawDependency[] {\n  const deps: RawDependency[] = [];\n\n  // Match single-line <PackageReference ... /> and multi-line <PackageReference ...>...</PackageReference>\n  // The regex captures the full element including potential child content\n  const elementRegex = /<PackageReference\\b([^>]*?)(?:\\/>|>([\\s\\S]*?)<\\/PackageReference>)/gi;\n  let match: RegExpExecArray | null;\n\n  while ((match = elementRegex.exec(content)) !== null) {\n    const attributes = match[1] ?? '';\n    const innerContent = match[2] ?? '';\n\n    // Extract the Include attribute (package name)\n    const includeMatch = attributes.match(/\\bInclude\\s*=\\s*\"([^\"]+)\"/i);\n    if (!includeMatch) {\n      continue;\n    }\n    const name = includeMatch[1].trim();\n    if (!name) {\n      logWarn(`[sec:nuget] Empty Include attribute in PackageReference at ${relativeManifest} \u2014 skipping`);\n      continue;\n    }\n\n    // Determine scope: PrivateAssets=\"all\" indicates a development/build-only dependency\n    const privateAssetsMatch = attributes.match(/\\bPrivateAssets\\s*=\\s*\"([^\"]*)\"/i);\n    const scope: ParsedDependency['scope'] =\n      privateAssetsMatch && privateAssetsMatch[1].toLowerCase() === 'all'\n        ? 'development'\n        : 'production';\n\n    // Extract version from Version attribute (inline format)\n    let constraint: string | null = null;\n    const versionAttrMatch = attributes.match(/\\bVersion\\s*=\\s*\"([^\"]+)\"/i);\n    if (versionAttrMatch && versionAttrMatch[1].trim() !== '') {\n      constraint = versionAttrMatch[1].trim();\n    }\n\n    // If no inline version, check for <Version> child element (multi-line format)\n    if (!constraint && innerContent) {\n      const versionElemMatch = innerContent.match(/<Version\\s*>\\s*([^<]+)\\s*<\\/Version>/i);\n      if (versionElemMatch && versionElemMatch[1].trim() !== '') {\n        constraint = versionElemMatch[1].trim();\n      }\n    }\n\n    if (!constraint) {\n      // Version may be managed centrally (Directory.Packages.props) \u2014 use \"*\"\n      constraint = '*';\n    }\n\n    deps.push({ name, constraint, scope });\n  }\n\n  return deps;\n}\n\n/**\n * Extract package entries from a legacy packages.config XML file.\n *\n * Format: `<package id=\"Newtonsoft.Json\" version=\"13.0.1\" targetFramework=\"net48\" />`\n * All packages from packages.config are treated as production scope.\n */\nfunction extractPackagesConfig(content: string, relativeManifest: string): RawDependency[] {\n  const deps: RawDependency[] = [];\n\n  const packageRegex = /<package\\b([^>]*?)\\/>/gi;\n  let match: RegExpExecArray | null;\n\n  while ((match = packageRegex.exec(content)) !== null) {\n    const attributes = match[1] ?? '';\n\n    const idMatch = attributes.match(/\\bid\\s*=\\s*\"([^\"]+)\"/i);\n    if (!idMatch) continue;\n    const name = idMatch[1].trim();\n    if (!name) {\n      logWarn(`[sec:nuget] Empty id attribute in packages.config at ${relativeManifest} \u2014 skipping`);\n      continue;\n    }\n\n    const versionMatch = attributes.match(/\\bversion\\s*=\\s*\"([^\"]+)\"/i);\n    const constraint = versionMatch && versionMatch[1].trim() !== '' ? versionMatch[1].trim() : '*';\n\n    deps.push({ name, constraint, scope: 'production' });\n  }\n\n  return deps;\n}\n\n/**\n * Attempt to load resolved versions from packages.lock.json in the given directory.\n * Returns an empty map if the lock file is not available.\n *\n * packages.lock.json format:\n * ```json\n * {\n *   \"version\": 1,\n *   \"dependencies\": {\n *     \"net8.0\": {\n *       \"Newtonsoft.Json\": {\n *         \"type\": \"Direct\",\n *         \"resolved\": \"13.0.3\",\n *         ...\n *       }\n *     }\n *   }\n * }\n * ```\n */\nfunction loadResolvedVersions(manifestDir: string): ResolvedVersionMap {\n  const map: ResolvedVersionMap = new Map();\n\n  const lockPath = path.join(manifestDir, 'packages.lock.json');\n  if (!fs.existsSync(lockPath)) {\n    return map;\n  }\n\n  try {\n    const raw = fs.readFileSync(lockPath, 'utf8');\n    const parsed = JSON.parse(raw);\n    extractFromPackagesLock(parsed, map);\n  } catch (err) {\n    logWarn(`[sec:nuget] Failed to parse packages.lock.json: ${err instanceof Error ? err.message : String(err)}`);\n  }\n\n  return map;\n}\n\n/**\n * Extract resolved versions from a parsed packages.lock.json object.\n *\n * Iterates over all target frameworks and their packages, storing\n * the `resolved` version for each package (keyed by lower-cased name).\n */\nfunction extractFromPackagesLock(\n  parsed: unknown,\n  map: ResolvedVersionMap,\n): void {\n  if (typeof parsed !== 'object' || parsed === null) return;\n\n  const root = parsed as Record<string, unknown>;\n  const dependencies = root['dependencies'];\n  if (typeof dependencies !== 'object' || dependencies === null) return;\n\n  // Iterate over target frameworks (e.g. \"net8.0\", \"net48\")\n  for (const framework of Object.values(dependencies as Record<string, unknown>)) {\n    if (typeof framework !== 'object' || framework === null) continue;\n\n    // Iterate over packages within the framework\n    for (const [packageName, packageInfo] of Object.entries(framework as Record<string, unknown>)) {\n      if (map.has(packageName.toLowerCase())) continue; // first occurrence wins\n      if (typeof packageInfo !== 'object' || packageInfo === null) continue;\n\n      const info = packageInfo as Record<string, unknown>;\n      const resolved = info['resolved'];\n      if (typeof resolved === 'string' && resolved.trim() !== '') {\n        map.set(packageName.toLowerCase(), resolved.trim());\n      }\n    }\n  }\n}\n\n/**\n * Extract the PackageLicenseExpression from a .csproj file.\n * Handles: <PackageLicenseExpression>MIT</PackageLicenseExpression>\n */\nfunction extractNugetLicense(content: string): string | undefined {\n  const match = content.match(/<PackageLicenseExpression\\s*>\\s*([^<]+)\\s*<\\/PackageLicenseExpression>/i);\n  if (match && match[1].trim() !== '') {\n    return match[1].trim();\n  }\n  return undefined;\n}\n"],
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+  "sourcesContent": ["/**\n * NuGet Version Extraction Plugin for KiroGraph-Sec\n *\n * Extends the existing architecture csproj parser to extract version constraints,\n * resolved versions (from packages.lock.json), and dependency scopes for security analysis.\n *\n * Reuses `csprojParser` from `src/architecture/manifest/csproj.ts` for discovery and\n * basic parsing, then layers on version/scope extraction.\n *\n * Handles:\n * - Inline attribute format: `<PackageReference Include=\"Name\" Version=\"1.0.0\"/>`\n * - Multi-line child element format: `<PackageReference Include=\"Name\"><Version>1.0.0</Version></PackageReference>`\n * - Legacy packages.config: `<package id=\"Name\" version=\"1.0.0\" targetFramework=\"...\"/>`\n * - Lock file packages.lock.json for resolved versions\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport type { ParsedDependency } from '../../types';\nimport { logWarn } from '../../../errors';\n\n/**\n * Resolved version map: package name (lower-cased) \u2192 resolved version string.\n * Built from packages.lock.json.\n */\ntype ResolvedVersionMap = Map<string, string>;\n\n/**\n * Parse a .csproj manifest and extract NuGet dependency declarations\n * with version constraints, scopes, and resolved versions from packages.lock.json.\n * Also parses a packages.config in the same directory if present.\n *\n * @param manifestPath - Absolute path to the .csproj file\n * @param projectRoot - Absolute path to the project root directory\n * @returns Array of parsed dependencies with version and scope information\n */\nexport async function parseNugetManifest(\n  manifestPath: string,\n  projectRoot: string,\n): Promise<ParsedDependency[]> {\n  const manifestDir = path.dirname(manifestPath);\n  const relativeManifest = path.relative(projectRoot, manifestPath).replace(/\\\\/g, '/');\n\n  // Read the .csproj content\n  let content: string;\n  try {\n    content = fs.readFileSync(manifestPath, 'utf8');\n  } catch (err) {\n    logWarn(`[sec:nuget] Failed to read ${relativeManifest}: ${err instanceof Error ? err.message : String(err)}`);\n    return [];\n  }\n\n  // Attempt to load resolved versions from packages.lock.json\n  const resolvedVersions = loadResolvedVersions(manifestDir);\n\n  // Extract project-level license from .csproj\n  const license = extractNugetLicense(content);\n\n  const dependencies: ParsedDependency[] = [];\n\n  // Extract from .csproj PackageReference elements\n  const csprojDeps = extractPackageReferences(content, relativeManifest);\n  for (const dep of csprojDeps) {\n    const resolvedVersion = resolvedVersions.get(dep.name.toLowerCase());\n    dependencies.push({\n      name: dep.name,\n      declaredConstraint: dep.constraint,\n      resolvedVersion,\n      scope: dep.scope,\n      ecosystem: 'nuget',\n      sourceManifest: relativeManifest,\n      ...(license !== undefined ? { license } : {}),\n    });\n  }\n\n  // Also parse packages.config in the same directory (legacy NuGet)\n  const packagesConfigPath = path.join(manifestDir, 'packages.config');\n  if (fs.existsSync(packagesConfigPath)) {\n    const relativePackagesConfig = path.relative(projectRoot, packagesConfigPath).replace(/\\\\/g, '/');\n    try {\n      const packagesConfigContent = fs.readFileSync(packagesConfigPath, 'utf8');\n      const legacyDeps = extractPackagesConfig(packagesConfigContent, relativePackagesConfig);\n      for (const dep of legacyDeps) {\n        const resolvedVersion = resolvedVersions.get(dep.name.toLowerCase());\n        dependencies.push({\n          name: dep.name,\n          declaredConstraint: dep.constraint,\n          resolvedVersion,\n          scope: dep.scope,\n          ecosystem: 'nuget',\n          sourceManifest: relativePackagesConfig,\n          ...(license !== undefined ? { license } : {}),\n        });\n      }\n    } catch (err) {\n      logWarn(`[sec:nuget] Failed to read ${relativePackagesConfig}: ${err instanceof Error ? err.message : String(err)}`);\n    }\n  }\n\n  // Transitive-only packages (present in packages.lock.json but never\n  // declared in the .csproj) would otherwise never become a Dependency_Node\n  // and would silently skip vulnerability scanning. resolvedVersions already\n  // has every package packages.lock.json resolved, direct or transitive\n  // (lower-cased \u2014 no original casing is retained by the lock parser).\n  const directNames = new Set(dependencies.map(d => d.name.toLowerCase()));\n  const lockRelativePath = path.relative(projectRoot, path.join(manifestDir, 'packages.lock.json')).replace(/\\\\/g, '/');\n  for (const [name, version] of resolvedVersions) {\n    if (directNames.has(name)) continue;\n    dependencies.push({\n      name,\n      declaredConstraint: version,\n      resolvedVersion: version,\n      scope: 'production',\n      ecosystem: 'nuget',\n      sourceManifest: lockRelativePath,\n    });\n  }\n\n  return dependencies;\n}\n\n/**\n * A raw dependency entry extracted from a .csproj or packages.config file.\n */\ninterface RawDependency {\n  name: string;\n  constraint: string;\n  scope: ParsedDependency['scope'];\n}\n\n/**\n * Extract PackageReference entries from .csproj XML content.\n *\n * Handles:\n * - Inline: `<PackageReference Include=\"Newtonsoft.Json\" Version=\"13.0.1\" />`\n * - With PrivateAssets=\"all\": `<PackageReference Include=\"MSTest.TestFramework\" Version=\"3.1.1\" PrivateAssets=\"all\" />`\n * - Multi-line child: `<PackageReference Include=\"Name\"><Version>1.0.0</Version></PackageReference>`\n */\nfunction extractPackageReferences(content: string, relativeManifest: string): RawDependency[] {\n  const deps: RawDependency[] = [];\n\n  // Match single-line <PackageReference ... /> and multi-line <PackageReference ...>...</PackageReference>\n  // The regex captures the full element including potential child content\n  const elementRegex = /<PackageReference\\b([^>]*?)(?:\\/>|>([\\s\\S]*?)<\\/PackageReference>)/gi;\n  let match: RegExpExecArray | null;\n\n  while ((match = elementRegex.exec(content)) !== null) {\n    const attributes = match[1] ?? '';\n    const innerContent = match[2] ?? '';\n\n    // Extract the Include attribute (package name)\n    const includeMatch = attributes.match(/\\bInclude\\s*=\\s*\"([^\"]+)\"/i);\n    if (!includeMatch) {\n      continue;\n    }\n    const name = includeMatch[1].trim();\n    if (!name) {\n      logWarn(`[sec:nuget] Empty Include attribute in PackageReference at ${relativeManifest} \u2014 skipping`);\n      continue;\n    }\n\n    // Determine scope: PrivateAssets=\"all\" indicates a development/build-only dependency\n    const privateAssetsMatch = attributes.match(/\\bPrivateAssets\\s*=\\s*\"([^\"]*)\"/i);\n    const scope: ParsedDependency['scope'] =\n      privateAssetsMatch && privateAssetsMatch[1].toLowerCase() === 'all'\n        ? 'development'\n        : 'production';\n\n    // Extract version from Version attribute (inline format)\n    let constraint: string | null = null;\n    const versionAttrMatch = attributes.match(/\\bVersion\\s*=\\s*\"([^\"]+)\"/i);\n    if (versionAttrMatch && versionAttrMatch[1].trim() !== '') {\n      constraint = versionAttrMatch[1].trim();\n    }\n\n    // If no inline version, check for <Version> child element (multi-line format)\n    if (!constraint && innerContent) {\n      const versionElemMatch = innerContent.match(/<Version\\s*>\\s*([^<]+)\\s*<\\/Version>/i);\n      if (versionElemMatch && versionElemMatch[1].trim() !== '') {\n        constraint = versionElemMatch[1].trim();\n      }\n    }\n\n    if (!constraint) {\n      // Version may be managed centrally (Directory.Packages.props) \u2014 use \"*\"\n      constraint = '*';\n    }\n\n    deps.push({ name, constraint, scope });\n  }\n\n  return deps;\n}\n\n/**\n * Extract package entries from a legacy packages.config XML file.\n *\n * Format: `<package id=\"Newtonsoft.Json\" version=\"13.0.1\" targetFramework=\"net48\" />`\n * All packages from packages.config are treated as production scope.\n */\nfunction extractPackagesConfig(content: string, relativeManifest: string): RawDependency[] {\n  const deps: RawDependency[] = [];\n\n  const packageRegex = /<package\\b([^>]*?)\\/>/gi;\n  let match: RegExpExecArray | null;\n\n  while ((match = packageRegex.exec(content)) !== null) {\n    const attributes = match[1] ?? '';\n\n    const idMatch = attributes.match(/\\bid\\s*=\\s*\"([^\"]+)\"/i);\n    if (!idMatch) continue;\n    const name = idMatch[1].trim();\n    if (!name) {\n      logWarn(`[sec:nuget] Empty id attribute in packages.config at ${relativeManifest} \u2014 skipping`);\n      continue;\n    }\n\n    const versionMatch = attributes.match(/\\bversion\\s*=\\s*\"([^\"]+)\"/i);\n    const constraint = versionMatch && versionMatch[1].trim() !== '' ? versionMatch[1].trim() : '*';\n\n    deps.push({ name, constraint, scope: 'production' });\n  }\n\n  return deps;\n}\n\n/**\n * Attempt to load resolved versions from packages.lock.json in the given directory.\n * Returns an empty map if the lock file is not available.\n *\n * packages.lock.json format:\n * ```json\n * {\n *   \"version\": 1,\n *   \"dependencies\": {\n *     \"net8.0\": {\n *       \"Newtonsoft.Json\": {\n *         \"type\": \"Direct\",\n *         \"resolved\": \"13.0.3\",\n *         ...\n *       }\n *     }\n *   }\n * }\n * ```\n */\nfunction loadResolvedVersions(manifestDir: string): ResolvedVersionMap {\n  const map: ResolvedVersionMap = new Map();\n\n  const lockPath = path.join(manifestDir, 'packages.lock.json');\n  if (!fs.existsSync(lockPath)) {\n    return map;\n  }\n\n  try {\n    const raw = fs.readFileSync(lockPath, 'utf8');\n    const parsed = JSON.parse(raw);\n    extractFromPackagesLock(parsed, map);\n  } catch (err) {\n    logWarn(`[sec:nuget] Failed to parse packages.lock.json: ${err instanceof Error ? err.message : String(err)}`);\n  }\n\n  return map;\n}\n\n/**\n * Extract resolved versions from a parsed packages.lock.json object.\n *\n * Iterates over all target frameworks and their packages, storing\n * the `resolved` version for each package (keyed by lower-cased name).\n */\nfunction extractFromPackagesLock(\n  parsed: unknown,\n  map: ResolvedVersionMap,\n): void {\n  if (typeof parsed !== 'object' || parsed === null) return;\n\n  const root = parsed as Record<string, unknown>;\n  const dependencies = root['dependencies'];\n  if (typeof dependencies !== 'object' || dependencies === null) return;\n\n  // Iterate over target frameworks (e.g. \"net8.0\", \"net48\")\n  for (const framework of Object.values(dependencies as Record<string, unknown>)) {\n    if (typeof framework !== 'object' || framework === null) continue;\n\n    // Iterate over packages within the framework\n    for (const [packageName, packageInfo] of Object.entries(framework as Record<string, unknown>)) {\n      if (map.has(packageName.toLowerCase())) continue; // first occurrence wins\n      if (typeof packageInfo !== 'object' || packageInfo === null) continue;\n\n      const info = packageInfo as Record<string, unknown>;\n      const resolved = info['resolved'];\n      if (typeof resolved === 'string' && resolved.trim() !== '') {\n        map.set(packageName.toLowerCase(), resolved.trim());\n      }\n    }\n  }\n}\n\n/**\n * Extract the PackageLicenseExpression from a .csproj file.\n * Handles: <PackageLicenseExpression>MIT</PackageLicenseExpression>\n */\nfunction extractNugetLicense(content: string): string | undefined {\n  const match = content.match(/<PackageLicenseExpression\\s*>\\s*([^<]+)\\s*<\\/PackageLicenseExpression>/i);\n  if (match && match[1].trim() !== '') {\n    return match[1].trim();\n  }\n  return undefined;\n}\n"],
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package/dist/security/manifest/plugins/pubspec.js

@@ -66,6 +66,18 @@ async function parsePubspecManifest(manifestPath, projectRoot) {
       });
     }
   }
+  const directNames = new Set(dependencies.map((d) => d.name));
+  for (const [name, version] of resolvedVersions) {
+    if (directNames.has(name)) continue;
+    dependencies.push({
+      name,
+      declaredConstraint: version,
+      resolvedVersion: version,
+      scope: "production",
+      ecosystem: "pub",
+      sourceManifest: relativeManifest
+    });
+  }
   return dependencies;
 }
 function extractSectionDependencies(content, sectionKey, relativeManifest) {

package/dist/security/manifest/plugins/pubspec.js.map

@@ -1,7 +1,7 @@
 {
   "version": 3,
   "sources": ["../../../../src/security/manifest/plugins/pubspec.ts"],
-  "sourcesContent": ["/**\n * Dart/Flutter pub Version Extraction Plugin for KiroGraph-Sec\n *\n * Parses pubspec.yaml manifests to extract Dart package declarations with\n * version constraints, scopes, and resolved versions from pubspec.lock.\n *\n * Uses lightweight regex-based YAML parsing \u2014 no external YAML library required.\n *\n * Handles:\n * - `dependencies:` section \u2192 'production' scope\n * - `dev_dependencies:` section \u2192 'development' scope\n * - Version formats: `^1.0.0`, `\">=1.0.0 <2.0.0\"`, `any`\n * - Skips SDK entries (`sdk:`), `flutter:`, path deps, and git deps\n */\nimport * as fs from 'fs';\nimport * as path from 'path';\nimport type { ParsedDependency } from '../../types';\nimport { logWarn } from '../../../errors';\n\n/**\n * Resolved version map: package name \u2192 resolved version string.\n * Built from pubspec.lock.\n */\ntype ResolvedVersionMap = Map<string, string>;\n\n/**\n * Parse a pubspec.yaml manifest and extract package declarations with\n * version constraints, scopes, and resolved versions from pubspec.lock.\n *\n * @param manifestPath - Absolute path to the pubspec.yaml file\n * @param projectRoot - Absolute path to the project root directory\n * @returns Array of parsed dependencies with version and scope information\n */\nexport async function parsePubspecManifest(\n  manifestPath: string,\n  projectRoot: string,\n): Promise<ParsedDependency[]> {\n  const manifestDir = path.dirname(manifestPath);\n  const relativeManifest = path.relative(projectRoot, manifestPath).replace(/\\\\/g, '/');\n\n  // Read the pubspec.yaml content\n  let content: string;\n  try {\n    content = fs.readFileSync(manifestPath, 'utf8');\n  } catch (err) {\n    logWarn(`[sec:pub] Failed to read ${relativeManifest}: ${err instanceof Error ? err.message : String(err)}`);\n    return [];\n  }\n\n  // Attempt to load resolved versions from pubspec.lock\n  const resolvedVersions = loadResolvedVersions(manifestDir);\n\n  // Extract the license field if present\n  const license = extractPubspecLicense(content);\n\n  const dependencies: ParsedDependency[] = [];\n\n  // Process `dependencies` (production) and `dev_dependencies` (development)\n  const sections: Array<{ key: string; scope: ParsedDependency['scope'] }> = [\n    { key: 'dependencies', scope: 'production' },\n    { key: 'dev_dependencies', scope: 'development' },\n  ];\n\n  for (const { key, scope } of sections) {\n    const sectionDeps = extractSectionDependencies(content, key, relativeManifest);\n    for (const dep of sectionDeps) {\n      const resolvedVersion = resolvedVersions.get(dep.name);\n      dependencies.push({\n        name: dep.name,\n        declaredConstraint: dep.constraint,\n        resolvedVersion,\n        scope,\n        ecosystem: 'pub',\n        sourceManifest: relativeManifest,\n        ...(license !== undefined ? { license } : {}),\n      });\n    }\n  }\n\n  return dependencies;\n}\n\n/**\n * A raw dependency entry extracted from a pubspec.yaml section.\n */\ninterface RawDependency {\n  name: string;\n  constraint: string;\n}\n\n/**\n * Extract dependencies from a specific top-level section of a pubspec.yaml file.\n * Uses indentation-based parsing to determine section boundaries.\n *\n * Section entries take one of three forms:\n * - `  package_name: ^1.0.0`      (inline scalar version)\n * - `  package_name: \">=1.0.0 <2.0.0\"` (quoted version)\n * - `  package_name: any`         (any version)\n * - `  package_name:`             (block mapping \u2014 path/git/sdk dep)\n *   `    path: ../local`\n *\n * Entries with sub-keys (block mappings) are skipped as non-registry deps.\n */\nfunction extractSectionDependencies(\n  content: string,\n  sectionKey: string,\n  relativeManifest: string,\n): RawDependency[] {\n  const deps: RawDependency[] = [];\n  const lines = content.split('\\n');\n\n  // Find the section header line (at column 0, no indent)\n  const headerPattern = new RegExp(`^${escapeRegex(sectionKey)}\\\\s*:\\\\s*$`);\n  let inSection = false;\n  let i = 0;\n\n  while (i < lines.length) {\n    const line = lines[i];\n    const trimmed = line.trimEnd();\n\n    // Detect section header\n    if (!inSection) {\n      if (headerPattern.test(trimmed)) {\n        inSection = true;\n      }\n      i++;\n      continue;\n    }\n\n    // Exit section when we encounter another top-level key (no leading whitespace)\n    if (trimmed !== '' && !/^\\s/.test(trimmed)) {\n      break;\n    }\n\n    // Skip blank lines inside section\n    if (trimmed === '') {\n      i++;\n      continue;\n    }\n\n    // Match a 2-space-indented package entry: `  package_name: ...`\n    const entryMatch = trimmed.match(/^  ([a-zA-Z0-9_][a-zA-Z0-9_.-]*):\\s*(.*)$/);\n    if (!entryMatch) {\n      i++;\n      continue;\n    }\n\n    const pkgName = entryMatch[1];\n    const valueOnSameLine = entryMatch[2].trim();\n\n    // Check if the next line has deeper indentation (block mapping \u2192 skip)\n    const nextLine = i + 1 < lines.length ? lines[i + 1] : '';\n    const isBlockMapping = nextLine !== '' && /^    \\S/.test(nextLine);\n\n    if (isBlockMapping) {\n      // Skip \u2014 path/git/sdk dependency; advance past the block\n      i++;\n      while (i < lines.length) {\n        const subLine = lines[i];\n        if (subLine.trimEnd() === '' || /^    /.test(subLine)) {\n          i++;\n        } else {\n          break;\n        }\n      }\n      continue;\n    }\n\n    // Skip SDK and flutter pseudo-packages\n    if (shouldSkipEntry(pkgName)) {\n      i++;\n      continue;\n    }\n\n    if (!isValidPackageName(pkgName)) {\n      logWarn(`[sec:pub] Invalid package name \"${pkgName}\" in ${relativeManifest} \u2014 skipping`);\n      i++;\n      continue;\n    }\n\n    const constraint = parseConstraintValue(valueOnSameLine);\n    deps.push({ name: pkgName, constraint });\n    i++;\n  }\n\n  return deps;\n}\n\n/**\n * Parse a pubspec.yaml dependency version value string.\n *\n * Handles:\n * - `^1.0.0` \u2192 `^1.0.0`\n * - `\">=1.0.0 <2.0.0\"` \u2192 `>=1.0.0 <2.0.0` (quotes stripped)\n * - `'>=1.0.0 <2.0.0'` \u2192 `>=1.0.0 <2.0.0`\n * - `any` \u2192 `*`\n * - empty \u2192 `*`\n */\nfunction parseConstraintValue(value: string): string {\n  if (!value || value === '' || value.toLowerCase() === 'any') return '*';\n\n  // Strip surrounding quotes\n  if ((value.startsWith('\"') && value.endsWith('\"')) ||\n      (value.startsWith(\"'\") && value.endsWith(\"'\"))) {\n    value = value.slice(1, -1).trim();\n  }\n\n  return value || '*';\n}\n\n/**\n * Determine whether a pubspec.yaml dependency key should be skipped.\n */\nfunction shouldSkipEntry(name: string): boolean {\n  if (name === 'sdk') return true;\n  if (name === 'flutter') return true;\n  return false;\n}\n\n/**\n * Validate that a pub package name follows Dart naming conventions.\n * Package names must be lowercase, with underscores, not hyphens.\n */\nfunction isValidPackageName(name: string): boolean {\n  if (!name || typeof name !== 'string') return false;\n  if (name.length > 128) return false;\n  return /^[a-zA-Z0-9_][a-zA-Z0-9_.-]*$/.test(name);\n}\n\n/**\n * Attempt to load resolved versions from pubspec.lock in the given directory.\n * Returns an empty map if pubspec.lock is not available.\n *\n * pubspec.lock YAML format:\n * ```yaml\n * packages:\n *   http:\n *     dependency: \"direct main\"\n *     description:\n *       name: http\n *       url: \"https://pub.dartlang.org\"\n *     version: \"0.13.5\"\n *   test:\n *     dependency: \"direct dev\"\n *     version: \"1.21.4\"\n * ```\n */\nfunction loadResolvedVersions(manifestDir: string): ResolvedVersionMap {\n  const map: ResolvedVersionMap = new Map();\n\n  const lockPath = path.join(manifestDir, 'pubspec.lock');\n  if (!fs.existsSync(lockPath)) {\n    return map;\n  }\n\n  try {\n    const lockContent = fs.readFileSync(lockPath, 'utf8');\n    extractFromPubspecLock(lockContent, map);\n  } catch (err) {\n    logWarn(`[sec:pub] Failed to parse pubspec.lock: ${err instanceof Error ? 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err.message : String(err)}`);\n    return [];\n  }\n\n  // Attempt to load resolved versions from pubspec.lock\n  const resolvedVersions = loadResolvedVersions(manifestDir);\n\n  // Extract the license field if present\n  const license = extractPubspecLicense(content);\n\n  const dependencies: ParsedDependency[] = [];\n\n  // Process `dependencies` (production) and `dev_dependencies` (development)\n  const sections: Array<{ key: string; scope: ParsedDependency['scope'] }> = [\n    { key: 'dependencies', scope: 'production' },\n    { key: 'dev_dependencies', scope: 'development' },\n  ];\n\n  for (const { key, scope } of sections) {\n    const sectionDeps = extractSectionDependencies(content, key, relativeManifest);\n    for (const dep of sectionDeps) {\n      const resolvedVersion = resolvedVersions.get(dep.name);\n      dependencies.push({\n        name: dep.name,\n        declaredConstraint: dep.constraint,\n        resolvedVersion,\n        scope,\n        ecosystem: 'pub',\n        sourceManifest: relativeManifest,\n        ...(license !== undefined ? { license } : {}),\n      });\n    }\n  }\n\n  // Transitive-only packages (present in pubspec.lock but never declared in\n  // pubspec.yaml) would otherwise never become a Dependency_Node and would\n  // silently skip vulnerability scanning. resolvedVersions already has every\n  // package pubspec.lock resolved, direct or transitive.\n  const directNames = new Set(dependencies.map(d => d.name));\n  for (const [name, version] of resolvedVersions) {\n    if (directNames.has(name)) continue;\n    dependencies.push({\n      name,\n      declaredConstraint: version,\n      resolvedVersion: version,\n      scope: 'production',\n      ecosystem: 'pub',\n      sourceManifest: relativeManifest,\n    });\n  }\n\n  return dependencies;\n}\n\n/**\n * A raw dependency entry extracted from a pubspec.yaml section.\n */\ninterface RawDependency {\n  name: string;\n  constraint: string;\n}\n\n/**\n * Extract dependencies from a specific top-level section of a pubspec.yaml file.\n * Uses indentation-based parsing to determine section boundaries.\n *\n * Section entries take one of three forms:\n * - `  package_name: ^1.0.0`      (inline scalar version)\n * - `  package_name: \">=1.0.0 <2.0.0\"` (quoted version)\n * - `  package_name: any`         (any version)\n * - `  package_name:`             (block mapping \u2014 path/git/sdk dep)\n *   `    path: ../local`\n *\n * Entries with sub-keys (block mappings) are skipped as non-registry deps.\n */\nfunction extractSectionDependencies(\n  content: string,\n  sectionKey: string,\n  relativeManifest: string,\n): RawDependency[] {\n  const deps: RawDependency[] = [];\n  const lines = content.split('\\n');\n\n  // Find the section header line (at column 0, no indent)\n  const headerPattern = new RegExp(`^${escapeRegex(sectionKey)}\\\\s*:\\\\s*$`);\n  let inSection = false;\n  let i = 0;\n\n  while (i < lines.length) {\n    const line = lines[i];\n    const trimmed = line.trimEnd();\n\n    // Detect section header\n    if (!inSection) {\n      if (headerPattern.test(trimmed)) {\n        inSection = true;\n      }\n      i++;\n      continue;\n    }\n\n    // Exit section when we encounter another top-level key (no leading whitespace)\n    if (trimmed !== '' && !/^\\s/.test(trimmed)) {\n      break;\n    }\n\n    // Skip blank lines inside section\n    if (trimmed === '') {\n      i++;\n      continue;\n    }\n\n    // Match a 2-space-indented package entry: `  package_name: ...`\n    const entryMatch = trimmed.match(/^  ([a-zA-Z0-9_][a-zA-Z0-9_.-]*):\\s*(.*)$/);\n    if (!entryMatch) {\n      i++;\n      continue;\n    }\n\n    const pkgName = entryMatch[1];\n    const valueOnSameLine = entryMatch[2].trim();\n\n    // Check if the next line has deeper indentation (block mapping \u2192 skip)\n    const nextLine = i + 1 < lines.length ? 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 }

package/dist/security/manifest/plugins/pyproject.js

@@ -89,6 +89,18 @@ async function parsePyprojectManifest(manifestPath, projectRoot) {
       });
     }
   }
+  const directNames = new Set(dependencies.map((d) => d.name.toLowerCase()));
+  for (const [name, version] of resolvedVersions) {
+    if (directNames.has(name)) continue;
+    dependencies.push({
+      name,
+      declaredConstraint: version,
+      resolvedVersion: version,
+      scope: "production",
+      ecosystem: "pypi",
+      sourceManifest: relativeManifest
+    });
+  }
   return dependencies;
 }
 function extractPep621Dependencies(content, relativeManifest) {